Variant report

Variant	rs13102085
Chromosome Location	chr4:10065886-10065887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:10020071..10021146-chr4:10064556..10066056,33	MCF-7	breast:
2	chr4:9766486..9767204-chr4:10064960..10065893,2	MCF-7	breast:
3	chr4:10065208..10068130-chr4:10069826..10072455,2	MCF-7	breast:
4	chr4:10019482..10021014-chr4:10065089..10066567,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109667	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10516200	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10939679	0.85[AFR][1000 genomes]
rs10939680	0.89[AFR][1000 genomes]
rs10939681	0.89[AFR][1000 genomes]
rs10939690	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11731597	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12108388	0.84[AFR][1000 genomes]
rs12500400	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12500653	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12503195	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12506004	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12646099	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13112782	0.89[AFR][1000 genomes]
rs13127630	0.89[AFR][1000 genomes]
rs13152337	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16868313	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16868326	0.85[EUR][1000 genomes]
rs2241470	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241475	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241476	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2241477	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241478	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2241480	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241486	0.93[EUR][1000 genomes]
rs34893238	0.93[EUR][1000 genomes]
rs35150828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756229	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775930	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3822248	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3822249	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6449265	0.94[ASN][1000 genomes]
rs6449266	0.91[ASN][1000 genomes]
rs6828198	0.92[ASN][1000 genomes]
rs6828222	0.92[ASN][1000 genomes]
rs6830786	0.93[EUR][1000 genomes]
rs734122	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7659924	0.89[AFR][1000 genomes]
rs7663448	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7676605	0.90[ASN][1000 genomes]
rs7683832	0.84[AFR][1000 genomes]
rs7685806	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533218	chr4:9371016-10252290	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
2	nsv530090	chr4:9383695-10165033	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	nsv1014216	chr4:9713612-10223836	Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
4	nsv1010249	chr4:9716101-10086188	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv878681	chr4:9802853-10397327	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
6	nsv997941	chr4:9805223-10493388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
7	nsv1008649	chr4:9805223-10589802	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	nsv1000587	chr4:9805223-10610752	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	nsv537022	chr4:9805223-10610752	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
10	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
11	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
12	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
13	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
15	nsv537026	chr4:9903566-10262258	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
16	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
17	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
18	esv2752052	chr4:9911872-10313111	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
19	nsv1010620	chr4:9937123-10686682	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
20	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
21	nsv532706	chr4:9948018-10451450	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
22	nsv1013022	chr4:9961220-10230042	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
23	nsv537028	chr4:9961220-10230042	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
24	nsv537029	chr4:9961220-10262258	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
25	nsv878691	chr4:9966477-10418078	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
26	nsv1013487	chr4:9972011-10320963	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
27	nsv829857	chr4:9982514-10155835	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
28	nsv469621	chr4:9987670-10142287	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
29	nsv482719	chr4:9987670-10142287	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
30	nsv1008067	chr4:10004664-10262258	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
31	nsv537030	chr4:10004664-10262258	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
32	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
33	nsv537031	chr4:10040713-10262258	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
34	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
35	nsv878692	chr4:10042160-10099333	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
36	nsv428438	chr4:10058226-10273779	Flanking Active TSS Genic enhancers Strong transcription Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13102085	SLC2A9	cis	Artery Tibial	GTEx
rs13102085	WDR1	Cis_1M	lymphoblastoid	RTeQTL
rs13102085	SLC2A9	cis	Whole Blood	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10035800-10068400	Weak transcription	Aorta	Aorta
2	chr4:10050000-10066400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:10051000-10068200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr4:10051400-10076200	Weak transcription	Small Intestine	intestine
5	chr4:10052200-10067800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:10054600-10068600	Weak transcription	Gastric	stomach
7	chr4:10056600-10074000	Weak transcription	HUVEC	blood vessel
8	chr4:10056800-10067800	Weak transcription	HSMM	muscle
9	chr4:10058000-10068400	Weak transcription	Psoas Muscle	Psoas
10	chr4:10058800-10066800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:10058800-10068600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:10060800-10067200	Weak transcription	Spleen	Spleen
13	chr4:10060800-10068600	Weak transcription	Ovary	ovary
14	chr4:10061000-10066600	Weak transcription	NH-A	brain
15	chr4:10061000-10066800	Weak transcription	Fetal Intestine Large	intestine
16	chr4:10061200-10067600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:10062000-10070600	Weak transcription	NHDF-Ad	bronchial
18	chr4:10062200-10068000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr4:10062200-10069400	Weak transcription	GM12878-XiMat	blood
20	chr4:10062400-10071600	Strong transcription	Primary T cells from cord blood	blood
21	chr4:10062600-10071600	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr4:10063000-10071400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr4:10063000-10071400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr4:10063000-10071400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr4:10063200-10072400	Weak transcription	A549	lung
26	chr4:10063800-10067800	Weak transcription	HSMMtube	muscle
27	chr4:10064000-10067800	Weak transcription	Fetal Thymus	thymus
28	chr4:10064000-10074000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:10064000-10075600	Weak transcription	Colonic Mucosa	Colon
30	chr4:10064200-10066000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr4:10064200-10066000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr4:10064400-10066000	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr4:10064400-10066600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:10064400-10069000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:10064600-10066000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr4:10064600-10066200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:10064600-10066800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr4:10064600-10071200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:10064600-10093800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:10064800-10066000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr4:10064800-10066000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr4:10064800-10066000	Enhancers	Brain Anterior Caudate	brain
43	chr4:10064800-10071400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr4:10065000-10066000	Enhancers	Colon Smooth Muscle	Colon
45	chr4:10065000-10066000	Enhancers	Rectal Smooth Muscle	rectum
46	chr4:10065000-10066000	Enhancers	Right Atrium	heart
47	chr4:10065000-10066000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr4:10065000-10066200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr4:10065000-10071400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:10065200-10066000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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