Variant report

Variant	rs10250659
Chromosome Location	chr7:3952043-3952044
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 156 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs10085400	1.00[JPT][hapmap]
rs10085568	1.00[JPT][hapmap]
rs1013880	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10215004	0.80[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10215340	0.86[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10241703	1.00[JPT][hapmap]
rs10242459	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs10244636	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs10245389	0.87[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10246449	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs10249255	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10252169	0.85[JPT][hapmap]
rs10254099	1.00[JPT][hapmap]
rs10256741	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs10262942	0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10263496	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10267786	1.00[JPT][hapmap]
rs10273444	1.00[JPT][hapmap]
rs10479833	1.00[JPT][hapmap]
rs10479834	1.00[JPT][hapmap]
rs10485864	0.88[CEU][hapmap]
rs10951315	0.82[JPT][hapmap]
rs10951322	0.85[JPT][hapmap]
rs10951336	1.00[JPT][hapmap]
rs10951368	0.87[ASN][1000 genomes]
rs10951374	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11514766	0.87[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11971293	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11973380	0.88[ASN][1000 genomes]
rs11974190	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs11974357	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11976915	1.00[JPT][hapmap]
rs11977993	1.00[JPT][hapmap]
rs11980947	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11982345	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11983563	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12531046	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12531980	0.85[JPT][hapmap]
rs12531984	0.82[JPT][hapmap]
rs12532040	0.85[JPT][hapmap]
rs12532171	0.94[CEU][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12532903	1.00[JPT][hapmap]
rs12532912	1.00[JPT][hapmap]
rs12533946	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12536445	1.00[JPT][hapmap]
rs12537696	1.00[JPT][hapmap]
rs12538997	1.00[JPT][hapmap]
rs12539695	0.82[JPT][hapmap]
rs12540101	1.00[JPT][hapmap]
rs12690803	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12690804	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs12701219	1.00[JPT][hapmap]
rs12701221	1.00[JPT][hapmap]
rs12701229	1.00[JPT][hapmap]
rs12701262	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12701271	0.88[ASN][1000 genomes]
rs12701272	0.88[ASN][1000 genomes]
rs13221624	1.00[JPT][hapmap]
rs13236653	1.00[JPT][hapmap]
rs13236719	0.85[JPT][hapmap]
rs13245096	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1476644	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1548612	1.00[JPT][hapmap]
rs1548613	0.82[JPT][hapmap]
rs1548614	0.82[JPT][hapmap]
rs17133859	0.84[JPT][hapmap]
rs17259867	0.82[JPT][hapmap]
rs17259924	0.82[JPT][hapmap]
rs17261199	1.00[JPT][hapmap]
rs17325709	0.82[JPT][hapmap]
rs1962783	1.00[JPT][hapmap]
rs1962784	1.00[JPT][hapmap]
rs1962785	1.00[JPT][hapmap]
rs2007554	1.00[JPT][hapmap]
rs2057920	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs2057921	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs2079376	0.87[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2341959	1.00[JPT][hapmap]
rs2880159	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2880204	1.00[JPT][hapmap]
rs41873	1.00[JPT][hapmap]
rs4431501	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs6462361	0.85[JPT][hapmap]
rs6462401	0.93[CEU][hapmap]
rs6462407	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs6462411	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6462413	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6462447	0.82[CEU][hapmap]
rs6943646	0.82[JPT][hapmap]
rs6944393	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6945778	0.85[JPT][hapmap]
rs6948552	1.00[JPT][hapmap]
rs6952864	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6953282	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs6953604	1.00[JPT][hapmap]
rs6953707	0.88[ASN][1000 genomes]
rs6955650	1.00[JPT][hapmap]
rs6956020	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6956479	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6957166	1.00[JPT][hapmap]
rs6958535	1.00[JPT][hapmap]
rs6959492	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6959674	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6959835	1.00[JPT][hapmap]
rs6961230	0.85[JPT][hapmap]
rs6961561	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs6962058	0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6962389	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6962750	0.88[ASN][1000 genomes]
rs6963674	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs6966030	1.00[JPT][hapmap]
rs6968948	1.00[JPT][hapmap]
rs6969052	1.00[JPT][hapmap]
rs6970116	1.00[JPT][hapmap]
rs6971803	1.00[JPT][hapmap]
rs6971828	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6971873	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6971953	1.00[JPT][hapmap]
rs6972806	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6973944	0.82[JPT][hapmap]
rs6975313	0.82[JPT][hapmap]
rs6975723	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs6977305	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6977844	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6978964	0.85[JPT][hapmap]
rs6979937	0.85[JPT][hapmap]
rs6980085	1.00[JPT][hapmap]
rs768721	0.82[JPT][hapmap]
rs7778705	1.00[JPT][hapmap]
rs7783415	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7786556	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7791274	0.82[JPT][hapmap]
rs7794504	1.00[JPT][hapmap]
rs7800775	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7804166	1.00[JPT][hapmap]
rs7807003	1.00[JPT][hapmap]
rs874344	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs917168	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs917198	0.85[JPT][hapmap]
rs9655007	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9655343	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs9655348	1.00[JPT][hapmap]
rs9886069	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9886234	0.87[ASN][1000 genomes]
rs9986911	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1029406	chr7:3860894-4477095	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538685	chr7:3860894-4477095	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026410	chr7:3869104-4383606	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1025497	chr7:3905444-4176032	Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv538686	chr7:3905444-4176032	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv433014	chr7:3910039-4054769	Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv518377	chr7:3939055-3978342	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1030082	chr7:3941203-3986403	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1020222	chr7:3946655-3985756	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1027500	chr7:3949954-3986403	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3901200-3959600	Weak transcription	Pancreas	Pancrea
2	chr7:3936800-3974200	Weak transcription	Aorta	Aorta
3	chr7:3940600-3953800	Weak transcription	Fetal Brain Male	brain
4	chr7:3948200-3955000	Weak transcription	Spleen	Spleen
5	chr7:3948800-3953000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr7:3949200-3952200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr7:3950200-3952200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:3950200-3953600	Weak transcription	Fetal Brain Female	brain
9	chr7:3950400-3952400	Enhancers	Brain Anterior Caudate	brain
10	chr7:3950400-3952600	Enhancers	Brain Cingulate Gyrus	brain
11	chr7:3950600-3952200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:3950600-3952800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr7:3950600-3953000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:3950600-3955600	Weak transcription	Brain Angular Gyrus	brain
15	chr7:3950600-3955800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr7:3950800-3952200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr7:3950800-3952400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr7:3950800-3952400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr7:3950800-3952400	Enhancers	NHEK	skin
20	chr7:3951000-3955400	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:3951000-3955600	Weak transcription	Brain Substantia Nigra	brain
22	chr7:3951000-3955800	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr7:3951200-3954600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr7:3951400-3952400	Enhancers	NH-A	brain
25	chr7:3951400-3953600	Enhancers	Fetal Lung	lung
26	chr7:3951600-3952200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr7:3951600-3952400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:3951600-3952400	Enhancers	Brain Germinal Matrix	brain
29	chr7:3951600-3954000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr7:3951800-3952400	Enhancers	Adipose Nuclei	Adipose
31	chr7:3952000-3952200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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