Variant report

Variant	rs1005678
Chromosome Location	chr3:50210289-50210290
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr3:50209732-50210513	Hela-S3	cervix:	n/a	chr3:50210046-50210066 chr3:50209979-50209990 chr3:50210050-50210061 chr3:50210052-50210060
2	TCF7L2	chr3:50210040-50210544	Hela-S3	cervix:	n/a	chr3:50210403-50210417

No.	Distal block	Cell Line	Cell type
1	chr3:50194586..50199661-chr3:50206741..50210376,5	K562	blood:
2	chr3:50164983..50167115-chr3:50208238..50210374,2	MCF-7	breast:
3	chr3:50191401..50200098-chr3:50206213..50213809,14	MCF-7	breast:
4	chr3:50191627..50193691-chr3:50209687..50211278,2	MCF-7	breast:

Variant related genes	Relation type
SEMA3F	TF binding region
MIR566	TF binding region
ENSG00000235016	Chromatin interaction
ENSG00000001617	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11130248	0.81[CHB][hapmap]
rs12054052	0.87[ASN][1000 genomes]
rs12054403	0.85[CHB][hapmap]
rs12485390	0.82[CHB][hapmap]
rs12485909	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs12487392	0.84[ASN][1000 genomes]
rs12488302	0.85[CHB][hapmap]
rs12491177	0.82[ASN][1000 genomes]
rs12494414	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs12632110	0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12721544	0.86[ASN][1000 genomes]
rs2021734	0.88[ASN][1000 genomes]
rs2071203	0.81[CHB][hapmap]
rs2071204	0.81[CHB][hapmap]
rs2072053	0.89[ASN][1000 genomes]
rs2072054	0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2073500	0.81[CHB][hapmap]
rs2188151	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2233476	0.81[CHB][hapmap]
rs2236940	0.81[CHB][hapmap]
rs2236941	0.81[CHB][hapmap]
rs2236944	0.81[CHB][hapmap]
rs2236946	0.81[CHB][hapmap]
rs2269430	0.82[CHB][hapmap]
rs2269432	0.82[CHB][hapmap]
rs2285043	0.81[CHB][hapmap]
rs2285044	0.82[CHB][hapmap]
rs2298953	0.81[CHB][hapmap]
rs2298954	0.81[CHB][hapmap]
rs2518795	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2518796	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2526389	0.83[EUR][1000 genomes]
rs2624838	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2624839	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213621	0.81[CHB][hapmap]
rs35455589	0.81[CHB][hapmap]
rs35587949	0.81[CHB][hapmap]
rs3774739	0.86[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs3774741	0.89[ASN][1000 genomes]
rs3774748	0.92[ASN][1000 genomes]
rs3774752	0.90[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs3774753	0.81[CHB][hapmap]
rs3774755	0.81[CHB][hapmap]
rs4141407	0.82[CHB][hapmap]
rs4688679	0.81[CHB][hapmap]
rs4688682	0.81[CHB][hapmap]
rs4688683	0.82[ASN][1000 genomes]
rs4688724	0.82[CHB][hapmap]
rs4688732	0.81[CHB][hapmap]
rs4688734	0.81[CHB][hapmap]
rs4688741	0.81[CHB][hapmap]
rs4688746	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs4688747	0.89[ASN][1000 genomes]
rs58137261	0.86[ASN][1000 genomes]
rs58191283	0.85[ASN][1000 genomes]
rs60276643	0.82[ASN][1000 genomes]
rs6800021	0.92[EUR][1000 genomes]
rs7645537	0.81[CHB][hapmap]
rs9830408	0.82[CHB][hapmap]
rs9882618	0.83[ASN][1000 genomes]
rs9883222	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv432418	chr3:50114496-50224196	Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
7	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription 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 miRNA target site	94 gene(s)	inside rSNPs	diseases
10	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
11	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
12	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
13	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
15	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
16	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
17	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
19	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
20	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
21	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
22	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking 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 miRNA target site	53 gene(s)	inside rSNPs	diseases
23	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
24	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
25	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
26	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
27	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
28	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1005678	RBM6	cis	Artery Tibial	GTEx
rs1005678	RBM6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50195400-50210600	Enhancers	Left Ventricle	heart
2	chr3:50195400-50210800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:50196200-50211600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr3:50197200-50211600	Genic enhancers	Esophagus	oesophagus
5	chr3:50200000-50210400	Enhancers	Fetal Brain Male	brain
6	chr3:50200600-50211800	Enhancers	Right Ventricle	heart
7	chr3:50202000-50210600	Enhancers	A549	lung
8	chr3:50202200-50210400	Enhancers	Lung	lung
9	chr3:50202800-50211000	Enhancers	Fetal Muscle Leg	muscle
10	chr3:50203400-50211400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:50204400-50211000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:50204600-50226600	Weak transcription	Brain Anterior Caudate	brain
13	chr3:50204800-50210400	Enhancers	Stomach Smooth Muscle	stomach
14	chr3:50204800-50210600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:50204800-50211200	Weak transcription	Aorta	Aorta
16	chr3:50204800-50211800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:50205000-50212800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:50205400-50211800	Enhancers	Stomach Mucosa	stomach
19	chr3:50205400-50226600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:50205400-50226600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:50205600-50211200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:50205600-50211400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:50205800-50211800	Weak transcription	Fetal Kidney	kidney
24	chr3:50206400-50226600	Weak transcription	NHLF	lung
25	chr3:50206600-50211200	Weak transcription	Ovary	ovary
26	chr3:50206600-50211600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr3:50207200-50211600	Enhancers	Spleen	Spleen
28	chr3:50208200-50210600	Enhancers	Fetal Heart	heart
29	chr3:50208200-50211200	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:50208200-50211600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:50208400-50210600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:50208400-50210600	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr3:50208400-50211400	Enhancers	Colonic Mucosa	Colon
34	chr3:50208600-50210400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr3:50208600-50210400	Enhancers	Psoas Muscle	Psoas
36	chr3:50208600-50211200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:50208600-50211200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr3:50208600-50211200	Enhancers	Fetal Muscle Trunk	muscle
39	chr3:50208600-50217000	Weak transcription	K562	blood
40	chr3:50208800-50210400	Enhancers	Pancreas	Pancrea
41	chr3:50208800-50211200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:50208800-50211200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:50208800-50211200	Weak transcription	Adipose Nuclei	Adipose
44	chr3:50208800-50211200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr3:50208800-50211600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:50208800-50212600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:50208800-50226600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:50208800-50226600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:50208800-50226600	Weak transcription	Osteobl	bone
50	chr3:50209000-50210400	Enhancers	Liver	Liver

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