Variant report

Variant	rs10160703
Chromosome Location	chr11:3893213-3893214
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3875167..3877402-chr11:3891084..3894016,3	K562	blood:
2	chr11:3892574..3897220-chr11:3897647..3902052,8	K562	blood:
3	chr11:3857978..3860215-chr11:3891494..3894175,2	K562	blood:
4	chr11:3892544..3895447-chr11:3927385..3929992,2	K562	blood:

Variant related genes	Relation type
ENSG00000229368	Chromatin interaction
ENSG00000228661	Chromatin interaction
ENSG00000263421	Chromatin interaction
ENSG00000167323	Chromatin interaction
ENSG00000177105	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10160254	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10160331	0.99[ASN][1000 genomes]
rs10160415	0.99[ASN][1000 genomes]
rs10160753	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767681	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10767684	0.99[ASN][1000 genomes]
rs10767685	0.93[ASN][1000 genomes]
rs10835217	0.88[ASN][1000 genomes]
rs10835226	0.99[ASN][1000 genomes]
rs10835231	0.99[ASN][1000 genomes]
rs10835232	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835236	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10835238	0.99[ASN][1000 genomes]
rs10835239	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10835245	0.99[ASN][1000 genomes]
rs10835246	0.99[ASN][1000 genomes]
rs10835247	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835248	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835250	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835252	0.99[ASN][1000 genomes]
rs10835256	0.98[ASN][1000 genomes]
rs10835261	0.96[ASN][1000 genomes]
rs10835262	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11030106	1.00[YRI][hapmap]
rs11030122	0.89[ASN][1000 genomes]
rs11030176	0.99[ASN][1000 genomes]
rs11030209	1.00[JPT][hapmap]
rs11030211	0.85[JPT][hapmap]
rs12275981	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1869084	0.87[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap]
rs1869085	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.99[ASN][1000 genomes]
rs1964492	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4414209	0.89[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4598668	0.85[JPT][hapmap]
rs4622250	1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4910584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7111609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7113148	1.00[JPT][hapmap]
rs7118295	0.98[ASN][1000 genomes]
rs7120336	0.99[ASN][1000 genomes]
rs7126870	0.80[ASN][1000 genomes]
rs7131437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7131469	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription 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 miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1046325	chr11:3856201-3895148	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv1039059	chr11:3856201-3909415	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv540910	chr11:3856201-3909415	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
12	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
13	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10160703	FAM160A2	cis	cerebellum	SCAN
rs10160703	OR56A1	cis	parietal	SCAN
rs10160703	TRIM21	cis	cerebellum	SCAN
rs10160703	TRIM22	cis	parietal	SCAN
rs10160703	OR56A5	cis	cerebellum	SCAN
rs10160703	POLR2L	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3883000-3893400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr11:3883200-3893600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr11:3883800-3893600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr11:3883800-3893800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:3886400-3893600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr11:3886600-3893400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr11:3886800-3899200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:3887200-3901400	Weak transcription	Brain Angular Gyrus	brain
9	chr11:3887400-3898600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr11:3888600-3911200	Weak transcription	Dnd41	blood
11	chr11:3889000-3893400	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr11:3889000-3898600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:3889000-3898600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:3889000-3899000	Weak transcription	Esophagus	oesophagus
15	chr11:3889000-3902400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr11:3889200-3913400	Weak transcription	Aorta	Aorta
17	chr11:3889400-3893400	Weak transcription	Thymus	Thymus
18	chr11:3889400-3894800	Weak transcription	Ovary	ovary
19	chr11:3889400-3894800	Weak transcription	Right Ventricle	heart
20	chr11:3889400-3896400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:3889400-3898200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr11:3889400-3898600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr11:3889400-3898600	Weak transcription	Pancreas	Pancrea
24	chr11:3889400-3898600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr11:3889400-3898800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:3889400-3898800	Weak transcription	Gastric	stomach
27	chr11:3889400-3899200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:3889400-3900000	Weak transcription	Right Atrium	heart
29	chr11:3889400-3901200	Weak transcription	Lung	lung
30	chr11:3889400-3901400	Weak transcription	Fetal Stomach	stomach
31	chr11:3889600-3894800	Weak transcription	Liver	Liver
32	chr11:3889600-3897200	Weak transcription	Colon Smooth Muscle	Colon
33	chr11:3889600-3897200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr11:3889600-3897600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:3889600-3898600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:3889600-3898600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr11:3889800-3894800	Weak transcription	Adipose Nuclei	Adipose
38	chr11:3889800-3894800	Weak transcription	Fetal Muscle Leg	muscle
39	chr11:3889800-3897600	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr11:3889800-3898600	Weak transcription	NHEK	skin
41	chr11:3889800-3899200	Weak transcription	Small Intestine	intestine
42	chr11:3889800-3901200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr11:3890000-3898600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:3890200-3898200	Weak transcription	Fetal Intestine Small	intestine
45	chr11:3890200-3898200	Weak transcription	Stomach Mucosa	stomach
46	chr11:3890400-3893600	Enhancers	Psoas Muscle	Psoas
47	chr11:3890600-3893400	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr11:3891200-3895600	Enhancers	Primary T cells fromperipheralblood	blood
49	chr11:3891400-3915000	Enhancers	Primary B cells from peripheral blood	blood
50	chr11:3891600-3893600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links