Variant report

Variant	rs1534520
Chromosome Location	chr7:121090859-121090860
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	chr7:121086464..121088878-chr7:121090558..121092067,2	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10215001	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10215613	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10215690	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10215696	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10224285	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10224531	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10229623	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10240942	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10255192	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10259018	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10264556	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10267770	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10270768	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11520945	0.82[EUR][1000 genomes]
rs11521035	0.82[EUR][1000 genomes]
rs11521036	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12706345	0.89[ASN][1000 genomes]
rs12706347	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12706348	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12706349	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13233332	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13237689	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13237707	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13237717	0.80[EUR][1000 genomes]
rs13242463	0.85[ASN][1000 genomes]
rs1406191	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1534519	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1534521	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1534522	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1609291	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1881373	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2049703	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2141357	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141359	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2178187	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2244845	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2244847	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2244849	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2263404	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2402564	0.91[ASN][1000 genomes]
rs2402565	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2402566	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2402567	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2463645	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2463646	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2697168	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2697171	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2697172	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2697173	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2697174	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2697188	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2697189	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2697190	0.87[ASN][1000 genomes]
rs2707484	0.89[ASN][1000 genomes]
rs2707485	0.84[ASN][1000 genomes]
rs2707490	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2707502	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28609751	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28623616	0.90[EUR][1000 genomes]
rs2950813	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2952571	0.85[ASN][1000 genomes]
rs2952573	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2952575	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2952577	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4507708	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4541839	0.81[EUR][1000 genomes]
rs4593469	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4731012	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4731013	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4731014	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4731015	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62476208	0.81[EUR][1000 genomes]
rs62476209	0.80[EUR][1000 genomes]
rs62476210	0.82[EUR][1000 genomes]
rs6466785	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67303703	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6961822	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6962156	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7776617	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7809856	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7809875	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9641666	0.81[EUR][1000 genomes]
rs9656282	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9656283	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9656284	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9656285	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9886342	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9942703	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv428507	chr7:121037303-121191934	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1029156	chr7:121069455-121143942	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv539104	chr7:121069455-121143942	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv1844602	chr7:121083616-121099167	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1534520	TSPAN12	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:121079000-121095800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:121087200-121091800	Weak transcription	Osteobl	bone
3	chr7:121088200-121091000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr7:121088400-121091800	Weak transcription	NHDF-Ad	bronchial
5	chr7:121089800-121091400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:121090600-121091800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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