Variant report

Variant	rs3899335
Chromosome Location	chr7:12347395-12347396
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10215270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10225682	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227871	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10228123	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10230889	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10231484	0.84[EUR][1000 genomes]
rs10231577	0.84[EUR][1000 genomes]
rs10236246	0.81[EUR][1000 genomes]
rs10239248	0.84[EUR][1000 genomes]
rs10247702	0.84[EUR][1000 genomes]
rs10248101	0.84[EUR][1000 genomes]
rs10251962	1.00[CEU][hapmap]
rs10256397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258758	0.84[EUR][1000 genomes]
rs10258988	0.84[EUR][1000 genomes]
rs10259305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10259332	0.90[EUR][1000 genomes]
rs10260491	0.84[EUR][1000 genomes]
rs10262667	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10262994	0.84[EUR][1000 genomes]
rs10264702	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10268302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10268480	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270435	1.00[CEU][hapmap]
rs10271597	1.00[CEU][hapmap]
rs10272812	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10273416	1.00[CEU][hapmap]
rs10273672	0.84[EUR][1000 genomes]
rs10273729	0.84[EUR][1000 genomes]
rs10274502	0.84[EUR][1000 genomes]
rs10275284	0.84[EUR][1000 genomes]
rs10275416	0.84[EUR][1000 genomes]
rs1030032	0.90[EUR][1000 genomes]
rs1079506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117386	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971213	0.85[EUR][1000 genomes]
rs11971413	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971590	1.00[CEU][hapmap]
rs11973540	0.84[EUR][1000 genomes]
rs11980307	1.00[ASN][1000 genomes]
rs13437654	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17165803	0.89[EUR][1000 genomes]
rs2017812	0.90[EUR][1000 genomes]
rs2160268	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs2192840	0.84[EUR][1000 genomes]
rs2216048	0.84[EUR][1000 genomes]
rs2287067	0.99[ASN][1000 genomes]
rs28564922	0.81[EUR][1000 genomes]
rs28572024	0.84[EUR][1000 genomes]
rs28608715	0.84[EUR][1000 genomes]
rs28657943	0.84[EUR][1000 genomes]
rs28722991	0.89[EUR][1000 genomes]
rs35472397	0.81[EUR][1000 genomes]
rs35612403	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35912436	0.81[EUR][1000 genomes]
rs3919542	0.84[EUR][1000 genomes]
rs3919543	0.84[EUR][1000 genomes]
rs4141568	0.84[EUR][1000 genomes]
rs4141569	0.84[EUR][1000 genomes]
rs4446632	0.84[EUR][1000 genomes]
rs4496864	0.84[EUR][1000 genomes]
rs4574747	0.84[EUR][1000 genomes]
rs61054154	0.84[EUR][1000 genomes]
rs6460920	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68050309	0.85[EUR][1000 genomes]
rs6944872	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6945381	0.84[EUR][1000 genomes]
rs6946459	1.00[CEU][hapmap]
rs6946838	0.85[EUR][1000 genomes]
rs6948209	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6948226	0.85[EUR][1000 genomes]
rs6948366	0.99[ASN][1000 genomes]
rs6948515	0.86[JPT][hapmap]
rs6949574	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6959666	0.84[EUR][1000 genomes]
rs6967342	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971849	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6972805	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs6977815	0.84[EUR][1000 genomes]
rs6977943	0.84[EUR][1000 genomes]
rs72584556	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72584562	0.84[EUR][1000 genomes]
rs72584563	0.84[EUR][1000 genomes]
rs72584564	0.84[EUR][1000 genomes]
rs72584567	0.84[EUR][1000 genomes]
rs72584570	0.84[EUR][1000 genomes]
rs72584572	0.84[EUR][1000 genomes]
rs72584573	0.84[EUR][1000 genomes]
rs72584574	0.84[EUR][1000 genomes]
rs72584575	0.84[EUR][1000 genomes]
rs72584589	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72584593	0.85[EUR][1000 genomes]
rs72586705	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72586714	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72586729	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7800111	0.85[EUR][1000 genomes]
rs7800823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7804012	0.81[EUR][1000 genomes]
rs7808979	0.86[JPT][hapmap]
rs918018	0.81[EUR][1000 genomes]
rs954660	1.00[CEU][hapmap]
rs9768757	0.84[EUR][1000 genomes]
rs984568	1.00[ASN][1000 genomes]

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	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv1033704	chr7:12286225-12355773	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv887629	chr7:12304555-12400837	ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1019021	chr7:12310445-12375516	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv887630	chr7:12323757-12400837	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1034059	chr7:12342549-12367818	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12338400-12359200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:12339600-12360000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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