Variant report

Variant	rs6716286
Chromosome Location	chr2:152576436-152576437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152575377..152577212-chr2:152579516..152582033,2	MCF-7	breast:
2	chr2:152573927..152576457-chr2:152683878..152686418,2	K562	blood:
3	chr2:152575075..152576644-chr2:152586756..152588663,2	K562	blood:

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10167462	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap]
rs10170273	0.94[CEU][hapmap];0.90[GIH][hapmap]
rs10172692	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10178880	0.94[CEU][hapmap];0.88[GIH][hapmap]
rs10185966	0.80[ASN][1000 genomes]
rs10193188	1.00[CEU][hapmap];0.95[GIH][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs1054883	0.94[CEU][hapmap];0.95[GIH][hapmap]
rs10930740	0.91[EUR][1000 genomes]
rs10930777	0.89[EUR][1000 genomes]
rs11695661	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs11896217	0.81[CHD][hapmap]
rs12052828	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12464543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12472627	0.81[GIH][hapmap]
rs12616767	0.94[CEU][hapmap];0.95[JPT][hapmap]
rs12620077	0.94[CEU][hapmap];0.88[GIH][hapmap]
rs12693090	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13015219	0.86[EUR][1000 genomes]
rs13032138	0.94[CEU][hapmap]
rs13404704	0.94[CEU][hapmap]
rs1357468	0.87[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap]
rs1523181	0.82[CHB][hapmap]
rs1799	0.94[CEU][hapmap];0.95[GIH][hapmap]
rs2344733	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs4077121	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs4077122	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs4273217	1.00[CEU][hapmap]
rs4274593	0.88[EUR][1000 genomes]
rs4289189	0.93[EUR][1000 genomes]
rs4300824	0.81[GIH][hapmap]
rs4309576	0.86[EUR][1000 genomes]
rs4349344	0.88[EUR][1000 genomes]
rs4355107	0.88[EUR][1000 genomes]
rs4358117	0.81[EUR][1000 genomes]
rs4374369	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4375863	0.97[EUR][1000 genomes]
rs4381781	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4413159	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4414677	0.81[GIH][hapmap]
rs4425075	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4453694	0.80[CHD][hapmap]
rs4465763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4508593	0.88[EUR][1000 genomes]
rs4508594	0.88[EUR][1000 genomes]
rs4536649	0.94[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap]
rs4564766	1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs4611637	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4614931	1.00[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs4625904	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4664066	0.83[CHB][hapmap]
rs4664494	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs4664497	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4664498	0.83[GIH][hapmap]
rs4664499	0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs4664501	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs4664502	0.89[EUR][1000 genomes]
rs6433566	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433569	0.97[GIH][hapmap];0.89[EUR][1000 genomes]
rs6433575	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6433603	0.87[EUR][1000 genomes]
rs6433606	0.87[EUR][1000 genomes]
rs6433610	0.88[EUR][1000 genomes]
rs6713162	0.94[CEU][hapmap];0.86[GIH][hapmap]
rs6715755	0.97[EUR][1000 genomes]
rs6723129	0.94[EUR][1000 genomes]
rs6729101	0.94[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs6730589	1.00[CEU][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes]
rs6733811	0.89[EUR][1000 genomes]
rs6733909	1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs6734148	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes]
rs6735208	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6741567	0.80[ASN][1000 genomes]
rs6747113	0.83[EUR][1000 genomes]
rs6760384	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs7424335	0.83[GIH][hapmap]
rs7426114	0.94[CEU][hapmap];0.88[GIH][hapmap]
rs7563441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7564024	0.93[CEU][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs7564674	0.93[EUR][1000 genomes]
rs7596744	0.94[CEU][hapmap];0.95[GIH][hapmap]
rs9287990	0.94[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][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	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv933357	chr2:152526786-152591138	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6716286	NEB	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152562200-152582000	Strong transcription	Fetal Muscle Trunk	muscle
2	chr2:152564600-152584000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:152575000-152577400	Weak transcription	Psoas Muscle	Psoas
4	chr2:152575600-152580600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
5	chr2:152575600-152582000	Strong transcription	Fetal Muscle Leg	muscle
6	chr2:152575800-152576800	Weak transcription	HSMMtube	muscle
7	chr2:152575800-152580400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
8	chr2:152575800-152584200	Weak transcription	Aorta	Aorta

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