Variant report

Variant	rs11175422
Chromosome Location	chr12:40561013-40561014
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	12:40560427-40561510..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10506148	0.83[CHB][hapmap]
rs10784340	1.00[CEU][hapmap]
rs10877913	1.00[CEU][hapmap]
rs10877955	1.00[CEU][hapmap]
rs10877971	1.00[CEU][hapmap]
rs10878123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10878208	0.84[ASN][1000 genomes]
rs11174831	1.00[CEU][hapmap]
rs11174928	1.00[CEU][hapmap]
rs11175102	1.00[CEU][hapmap]
rs11175103	1.00[CEU][hapmap]
rs11175256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11175260	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11175332	0.84[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11175371	0.85[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs11175401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175405	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs11175458	0.96[ASN][1000 genomes]
rs11175540	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175558	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11564115	1.00[JPT][hapmap]
rs12372213	1.00[CEU][hapmap]
rs12581285	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12581617	0.80[ASN][1000 genomes]
rs1388593	0.84[ASN][1000 genomes]
rs1388596	0.84[JPT][hapmap]
rs1472117	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1491922	0.84[ASN][1000 genomes]
rs1491923	0.84[ASN][1000 genomes]
rs1491924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1491925	0.86[ASN][1000 genomes]
rs1491939	0.84[JPT][hapmap]
rs1491942	0.95[JPT][hapmap]
rs17442157	1.00[CEU][hapmap]
rs17443199	0.85[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs17458613	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17461429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17518546	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1817817	0.80[ASN][1000 genomes]
rs1907630	0.84[ASN][1000 genomes]
rs1907631	0.84[ASN][1000 genomes]
rs1907634	0.80[ASN][1000 genomes]
rs2046931	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2131088	1.00[JPT][hapmap]
rs2172240	0.84[ASN][1000 genomes]
rs2172241	0.84[ASN][1000 genomes]
rs2201144	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2253736	0.81[ASN][1000 genomes]
rs2638244	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2638247	0.86[ASN][1000 genomes]
rs2638250	0.90[ASN][1000 genomes]
rs2638268	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2638269	0.81[ASN][1000 genomes]
rs2638270	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2638271	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2708426	0.84[ASN][1000 genomes]
rs2708436	0.81[ASN][1000 genomes]
rs2708437	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2708438	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2708441	0.80[ASN][1000 genomes]
rs2708463	0.82[ASN][1000 genomes]
rs2708465	0.85[ASN][1000 genomes]
rs2708478	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2723260	0.84[ASN][1000 genomes]
rs2723269	1.00[JPT][hapmap]
rs28365179	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs28365683	1.00[CEU][hapmap]
rs72644819	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7310104	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs949640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
5	esv3398206	chr12:40556364-40581392	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40557400-40564600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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