Variant report

Variant	rs902779
Chromosome Location	chr6:119000593-119000594
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11153752	0.86[JPT][hapmap]
rs11153763	0.86[JPT][hapmap]
rs11754023	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11755121	0.86[JPT][hapmap]
rs11756438	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs11756440	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs11968351	0.86[JPT][hapmap]
rs12194555	0.86[JPT][hapmap]
rs12199463	0.86[JPT][hapmap]
rs12206329	0.86[JPT][hapmap]
rs12208253	0.86[JPT][hapmap]
rs13192336	0.86[JPT][hapmap]
rs13220480	0.85[JPT][hapmap]
rs1343287	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688631	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17349329	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1771752	0.87[JPT][hapmap]
rs1771755	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1771756	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17825844	0.89[CEU][hapmap]
rs1844963	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844964	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1857312	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2046951	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2213856	0.86[JPT][hapmap]
rs2356492	0.86[JPT][hapmap]
rs2452262	0.87[JPT][hapmap]
rs2638529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638530	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2638532	0.83[ASN][1000 genomes]
rs2638533	0.83[ASN][1000 genomes]
rs2638541	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638550	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2638552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2798321	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2798325	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2798326	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798329	0.84[ASW][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3734381	0.86[JPT][hapmap]
rs3752581	0.86[JPT][hapmap]
rs4027595	0.96[CEU][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4945624	0.81[ASN][1000 genomes]
rs4946356	0.92[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55892056	0.89[ASN][1000 genomes]
rs56344535	0.85[ASN][1000 genomes]
rs57237379	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60497831	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6911599	0.87[GIH][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs6925641	0.86[JPT][hapmap]
rs6937176	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72962906	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72962938	0.81[ASN][1000 genomes]
rs7740645	0.85[JPT][hapmap]
rs7746210	0.92[CEU][hapmap]
rs7751467	0.86[JPT][hapmap]
rs7764388	0.83[ASN][1000 genomes]
rs794857	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs794859	0.81[ASN][1000 genomes]
rs794861	0.81[ASN][1000 genomes]
rs9320663	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9320665	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9481850	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs9489497	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973944	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1025403	chr6:118635123-119122551	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1025456	chr6:118669672-119058789	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription 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 target site	9 gene(s)	inside rSNPs	diseases
5	nsv1027444	chr6:118687556-119121660	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv538428	chr6:118687556-119121660	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv949321	chr6:118692304-119137658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv432958	chr6:118692307-119010307	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv1034448	chr6:118698169-119016383	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1025097	chr6:118699752-119058789	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
11	nsv532052	chr6:118711850-119057295	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv432959	chr6:118716318-119010307	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv604556	chr6:118722589-119065365	Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv949416	chr6:118772508-119033063	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv948980	chr6:118772508-119137658	Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats 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 target site	10 gene(s)	inside rSNPs	diseases
16	nsv604559	chr6:118786486-119113317	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv1022865	chr6:118786586-119058789	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
18	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs902779	SLC35F1	cis	cerebellum	SCAN
rs902779	C6orf204	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118986400-119001800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:118990600-119025400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:118991200-119000800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr6:118991200-119001000	Weak transcription	Fetal Thymus	thymus
5	chr6:118991200-119004400	Weak transcription	Primary B cells from cord blood	blood
6	chr6:118992400-119001600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:118994600-119000600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:118994800-119000600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:118994800-119001200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:118998800-119000800	Genic enhancers	Primary T cells from cord blood	blood
11	chr6:118998800-119001600	Weak transcription	K562	blood
12	chr6:118998800-119002600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr6:118999400-119002600	Enhancers	Stomach Mucosa	stomach
14	chr6:118999600-119015600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:118999600-119021600	Weak transcription	Thymus	Thymus
16	chr6:119000000-119000800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:119000000-119001000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:119000000-119001000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:119000000-119001000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:119000000-119001400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:119000000-119001600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:119000000-119002400	Enhancers	HMEC	breast
23	chr6:119000000-119002800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr6:119000200-119000600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:119000200-119000800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr6:119000200-119001000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:119000200-119001200	Enhancers	Osteobl	bone
28	chr6:119000200-119002200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:119000200-119002600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:119000200-119002800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr6:119000200-119003000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:119000400-119000800	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr6:119000400-119000800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:119000400-119000800	Enhancers	HSMMtube	muscle
35	chr6:119000400-119001000	Enhancers	NH-A	brain
36	chr6:119000400-119001200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:119000400-119002600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:119000400-119002600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:119000400-119002600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links