Variant report

Variant	rs10252169
Chromosome Location	chr7:3899866-3899867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 170 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10085400	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085568	0.85[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1013880	0.85[JPT][hapmap]
rs10215004	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs10215340	0.85[JPT][hapmap]
rs10228397	0.88[ASN][1000 genomes]
rs10241703	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10242459	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10243770	0.81[CHB][hapmap];0.90[ASN][1000 genomes]
rs10244636	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[MKK][hapmap];0.90[ASN][1000 genomes]
rs10245389	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs10246449	0.81[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs10250659	0.85[JPT][hapmap]
rs10254099	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10256741	0.81[CHB][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs10263496	0.85[JPT][hapmap]
rs10267786	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs10273444	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10479833	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10479834	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10480105	0.91[ASN][1000 genomes]
rs10485864	0.88[ASN][1000 genomes]
rs10951315	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs10951322	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs10951336	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs10951374	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs11514766	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs11973090	0.90[ASN][1000 genomes]
rs11974190	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs11976915	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs11977993	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11982345	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs11983563	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs12112335	0.80[CEU][hapmap];0.81[CHB][hapmap];0.81[MEX][hapmap]
rs12531046	0.85[JPT][hapmap]
rs12531980	0.89[CEU][hapmap];0.81[CHB][hapmap]
rs12532040	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12532171	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs12532903	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12532912	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12533946	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs12536445	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12536663	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12537696	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12538997	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12540101	0.94[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12540220	0.83[ASN][1000 genomes]
rs12690803	0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12690804	0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12701219	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs12701221	0.85[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.93[ASN][1000 genomes]
rs12701227	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12701229	0.85[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs12701262	0.85[JPT][hapmap]
rs13221624	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13236653	1.00[CEU][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13236719	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13245096	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1476644	0.85[JPT][hapmap]
rs1548612	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs17133859	1.00[CHB][hapmap]
rs17261199	0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1962783	0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1962784	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1962785	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2007554	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2057919	0.90[ASN][1000 genomes]
rs2057920	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2057921	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2079376	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs2079377	0.90[ASN][1000 genomes]
rs2079378	0.86[ASN][1000 genomes]
rs2097899	0.87[ASN][1000 genomes]
rs2097900	0.91[ASN][1000 genomes]
rs2341959	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs28491320	0.90[ASN][1000 genomes]
rs2880159	0.82[JPT][hapmap]
rs2880204	0.85[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs28845270	0.90[ASN][1000 genomes]
rs34614163	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34730154	0.88[ASN][1000 genomes]
rs34960833	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35261333	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35712888	0.89[ASN][1000 genomes]
rs41873	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4431501	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6462361	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6462407	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6462411	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6462412	0.90[ASN][1000 genomes]
rs6462413	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6462423	0.88[ASN][1000 genomes]
rs67665990	0.81[ASN][1000 genomes]
rs6944393	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs6944479	0.85[ASN][1000 genomes]
rs6945778	0.80[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs6948552	0.85[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];1.00[ASN][1000 genomes]
rs6952864	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6953036	0.91[ASN][1000 genomes]
rs6953282	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6953604	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs6954370	0.90[ASN][1000 genomes]
rs6955650	0.81[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs6956479	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6957166	0.94[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957676	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958385	0.90[ASN][1000 genomes]
rs6958535	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6959492	0.81[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs6959674	0.81[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs6959835	0.81[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs6961230	0.80[CEU][hapmap];0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs6961561	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6962058	0.82[JPT][hapmap]
rs6962389	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs6963058	0.90[ASN][1000 genomes]
rs6963674	0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6966030	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6968148	0.90[ASN][1000 genomes]
rs6968267	0.90[ASN][1000 genomes]
rs6968272	0.90[ASN][1000 genomes]
rs6968444	0.90[ASN][1000 genomes]
rs6968948	0.86[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs6969052	0.81[CHB][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.98[ASN][1000 genomes]
rs6969235	0.82[ASN][1000 genomes]
rs6970116	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6971639	0.90[ASN][1000 genomes]
rs6971803	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6971828	0.85[JPT][hapmap]
rs6971873	0.85[JPT][hapmap]
rs6971953	0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6972806	0.81[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6973944	0.94[CEU][hapmap];0.81[CHB][hapmap]
rs6975313	0.94[CEU][hapmap];0.81[CHB][hapmap]
rs6975723	0.81[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6977305	0.85[JPT][hapmap]
rs6977844	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6978060	0.90[ASN][1000 genomes]
rs6978318	0.90[ASN][1000 genomes]
rs6978964	0.94[CEU][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6979937	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs6980085	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs7778705	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7783415	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs7786556	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs7788747	0.82[ASN][1000 genomes]
rs7794504	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7800775	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7804166	0.81[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs7806494	0.88[ASN][1000 genomes]
rs7807003	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7809616	0.84[ASN][1000 genomes]
rs7811839	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs917168	0.81[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs917198	0.85[CEU][hapmap];0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs9655007	0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs9655343	0.81[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs9655347	0.88[ASN][1000 genomes]
rs9655348	0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs985186	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9986911	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1027624	chr7:3808366-3923408	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv538684	chr7:3808366-3923408	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv887336	chr7:3870810-3934909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv887337	chr7:3886254-3934909	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1019190	chr7:3896634-3943566	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10252169	TMEM184A	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3894800-3900600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:3894800-3901600	Weak transcription	Aorta	Aorta
3	chr7:3898200-3901000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:3899200-3900600	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links