Variant report

Variant	rs6953604
Chromosome Location	chr7:3868788-3868789
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:3848437..3851053-chr7:3868632..3870528,2	MCF-7	breast:

Extended variants
information (count: 161 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs10085400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10085568	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1013880	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10215004	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10215340	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10241703	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs10242459	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10243770	1.00[CHB][hapmap]
rs10244636	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs10245389	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10246449	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10250659	1.00[JPT][hapmap]
rs10252169	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]
rs10254099	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs10256741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10262942	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10263496	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10267786	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10273444	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs10479833	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10479834	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10480105	0.95[ASN][1000 genomes]
rs10951315	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10951322	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10951336	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10951374	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11514766	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11974190	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs11976915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11977993	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11980947	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11982345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11983563	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12112335	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[MEX][hapmap]
rs12531046	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12531980	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs12531984	0.82[JPT][hapmap]
rs12532040	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12532171	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs12532903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12532912	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs12533946	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12536445	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12536663	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12539695	0.82[JPT][hapmap]
rs12540101	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12540220	0.90[ASN][1000 genomes]
rs12690803	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs12690804	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12701219	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12701221	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12701227	0.93[ASN][1000 genomes]
rs12701229	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs12701262	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs13221624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13236653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13236719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13245096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1476644	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1548612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1548613	0.82[JPT][hapmap]
rs1548614	0.82[JPT][hapmap]
rs17133859	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs17259867	0.82[JPT][hapmap]
rs17259924	0.82[JPT][hapmap]
rs17261199	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17325709	0.82[JPT][hapmap]
rs1962783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1962784	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs1962785	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2007554	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2057920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2057921	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2079376	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2097900	0.91[ASN][1000 genomes]
rs2341959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2880159	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2880204	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs34614163	0.95[ASN][1000 genomes]
rs34960833	0.95[ASN][1000 genomes]
rs35261333	0.95[ASN][1000 genomes]
rs35712888	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41873	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4431501	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6462361	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6462407	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6462411	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6462413	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6462447	0.81[CHB][hapmap]
rs67665990	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6943646	0.82[JPT][hapmap]
rs6944393	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6944479	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6945778	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6948552	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6952864	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6953036	0.95[ASN][1000 genomes]
rs6953282	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6955650	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6956479	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6957166	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6957676	0.86[ASN][1000 genomes]
rs6958535	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6959492	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6959674	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6959835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6961230	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6961561	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6962058	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6962389	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6963674	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6966030	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6968948	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6969052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6969235	0.85[ASN][1000 genomes]
rs6970116	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6971803	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6971828	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6971873	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6971953	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6972806	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs6973944	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6975313	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6975723	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6977305	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6977844	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6978964	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6979937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6980085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs768721	0.82[JPT][hapmap]
rs7778705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7783415	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7786556	0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs7788747	0.85[ASN][1000 genomes]
rs7791274	0.82[JPT][hapmap]
rs7794504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7800775	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7804166	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7806494	0.95[ASN][1000 genomes]
rs7807003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811839	0.93[ASN][1000 genomes]
rs917168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs917198	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9655007	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9655343	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9655348	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs985186	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9986911	0.89[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv1021443	chr7:3705273-3889334	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	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
8	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
9	nsv521103	chr7:3860836-3868788	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	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
11	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6953604	TMEM184A	cis	cerebellum	SCAN
rs6953604	MAFK	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3848400-3882000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:3849400-3880600	Weak transcription	Aorta	Aorta
3	chr7:3861000-3886400	Weak transcription	Pancreas	Pancrea

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