Variant report

Variant	rs9865532
Chromosome Location	chr3:51144316-51144317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 156 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs10433609	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10865962	0.94[CEU][hapmap]
rs11130267	0.94[CEU][hapmap]
rs11130280	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[ASN][1000 genomes]
rs11130286	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs11706571	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs11715556	0.94[CEU][hapmap]
rs11919932	0.94[CEU][hapmap]
rs12488948	0.82[CHD][hapmap]
rs12491206	0.81[CHD][hapmap]
rs12494165	0.83[ASW][hapmap];0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs12496621	0.82[CHD][hapmap]
rs13061003	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs13062018	0.94[CEU][hapmap]
rs13064199	0.94[CEU][hapmap]
rs13069365	0.82[CEU][hapmap]
rs13079136	0.94[CEU][hapmap]
rs13079565	0.94[CEU][hapmap]
rs13080170	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13085827	0.94[CEU][hapmap]
rs13086922	0.94[CEU][hapmap]
rs13093289	0.94[CEU][hapmap]
rs1318649	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap]
rs13324500	0.94[CEU][hapmap]
rs1480360	0.88[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap]
rs1480362	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1480364	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs2061950	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2170178	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs2219891	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs2355943	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs28708817	0.86[ASN][1000 genomes]
rs28810453	0.84[ASN][1000 genomes]
rs2883809	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs34628582	0.94[CEU][hapmap]
rs35356497	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3856932	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4078296	0.81[CHD][hapmap]
rs4132022	0.87[CEU][hapmap]
rs4244696	0.94[CEU][hapmap]
rs4244704	0.94[CEU][hapmap]
rs4263323	0.94[CEU][hapmap]
rs4267675	0.94[CEU][hapmap]
rs4286453	0.94[CEU][hapmap]
rs4309763	0.94[CEU][hapmap]
rs4323036	0.82[CHD][hapmap]
rs4353834	0.81[EUR][1000 genomes]
rs4356848	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364203	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4367100	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs4373098	0.94[CEU][hapmap]
rs4377512	0.94[CEU][hapmap]
rs4434173	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4438692	0.94[CEU][hapmap]
rs4443210	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4446244	0.94[CEU][hapmap]
rs4475072	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[ASN][1000 genomes]
rs4478114	0.94[CEU][hapmap]
rs4488874	0.94[CEU][hapmap]
rs4505743	0.94[CEU][hapmap]
rs4511931	0.94[CEU][hapmap]
rs4511933	0.94[CEU][hapmap]
rs4530566	0.94[CEU][hapmap]
rs4555554	0.93[CEU][hapmap]
rs4560329	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4566574	0.94[CEU][hapmap]
rs4572801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4582086	0.94[CEU][hapmap]
rs4586853	0.94[CEU][hapmap]
rs4589968	0.94[CEU][hapmap]
rs4615113	0.94[CEU][hapmap]
rs4927960	0.94[CEU][hapmap]
rs4927961	0.82[CHD][hapmap]
rs4927969	0.89[ASN][1000 genomes]
rs4927970	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4927973	0.86[ASN][1000 genomes]
rs4927978	0.94[CEU][hapmap]
rs4927983	0.94[CEU][hapmap]
rs4974092	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs4974094	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs4974099	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs4974108	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs6445501	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6445549	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.86[ASN][1000 genomes]
rs6445600	0.94[CEU][hapmap]
rs6445601	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs6445604	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs6445717	0.94[CEU][hapmap]
rs6445750	0.94[CEU][hapmap]
rs6445779	0.94[CEU][hapmap]
rs6445802	0.91[CEU][hapmap]
rs6446011	0.94[CEU][hapmap]
rs6446118	0.94[CEU][hapmap]
rs6446167	0.94[CEU][hapmap]
rs6446168	0.94[CEU][hapmap]
rs6446243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6446245	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6768601	0.94[CEU][hapmap]
rs6771085	0.94[CEU][hapmap]
rs6772197	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6784455	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs6787773	0.94[CEU][hapmap]
rs6787805	0.88[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6793613	0.94[CEU][hapmap]
rs6793648	0.94[CEU][hapmap]
rs6795272	0.83[ASW][hapmap];0.94[CEU][hapmap]
rs6796642	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6796847	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs6799722	0.86[ASN][1000 genomes]
rs6800279	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6810241	0.94[CEU][hapmap]
rs7428086	0.94[CEU][hapmap]
rs7429035	0.94[CEU][hapmap]
rs7433217	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs7611873	0.94[CEU][hapmap]
rs7614171	0.94[CEU][hapmap]
rs7614317	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7614482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs7614881	0.94[CEU][hapmap]
rs7615291	0.94[CEU][hapmap]
rs7616967	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7618173	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7627266	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs7629420	0.94[CEU][hapmap]
rs7629433	0.94[CEU][hapmap]
rs7634799	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7638732	0.83[ASW][hapmap];0.94[CEU][hapmap]
rs7640263	0.93[CEU][hapmap]
rs7651141	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7652655	0.94[CEU][hapmap]
rs7652818	0.94[CEU][hapmap]
rs7653451	0.94[CEU][hapmap]
rs899750	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs9682672	0.94[CEU][hapmap]
rs9713241	0.93[CEU][hapmap]
rs9758600	0.91[CEU][hapmap]
rs9815781	0.87[ASN][1000 genomes]
rs9823942	0.94[CEU][hapmap]
rs9828200	0.94[CEU][hapmap]
rs9832672	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs9837334	1.00[CEU][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9839484	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9844581	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9847479	0.89[ASN][1000 genomes]
rs9850021	0.94[CEU][hapmap]
rs9856566	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9857727	0.94[CEU][hapmap]
rs9860403	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs9865363	0.81[EUR][1000 genomes]
rs9868870	0.94[CEU][hapmap]
rs9877188	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs995543	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv3447639	chr3:51129523-51158383	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9865532	HEMK1	cis	cerebellum	SCAN
rs9865532	TNNC1	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51121000-51145200	Weak transcription	Fetal Brain Male	brain
2	chr3:51142000-51145200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:51143000-51144400	Strong transcription	Brain Angular Gyrus	brain
4	chr3:51143000-51144800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:51143000-51145000	ZNF genes & repeats	Fetal Brain Female	brain
6	chr3:51143200-51144400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:51143200-51144400	Strong transcription	Brain Substantia Nigra	brain
8	chr3:51143200-51144600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:51143400-51144600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:51143800-51144400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:51144000-51145400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:51144000-51145600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:51144000-51146000	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:51144200-51144400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:51144200-51144400	ZNF genes & repeats	Brain Germinal Matrix	brain
16	chr3:51144200-51144400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
17	chr3:51144200-51145800	Weak transcription	Brain Anterior Caudate	brain
18	chr3:51144200-51145800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:51144200-51147000	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links