Variant report

Variant	rs1917821
Chromosome Location	chr10:50768203-50768204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50749402..50751390-chr10:50767694..50770332,2	K562	blood:
2	chr10:50768064..50770893-chr10:50771784..50774255,2	K562	blood:
3	chr10:50767252..50769904-chr10:50772463..50774658,3	MCF-7	breast:
4	chr10:50760373..50763303-chr10:50765007..50769387,4	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10776575	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10776581	0.87[ASN][1000 genomes]
rs10776583	0.81[EUR][1000 genomes]
rs10857504	0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10857506	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10857510	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11101144	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11101155	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11591393	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12146288	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1917820	0.82[EUR][1000 genomes]
rs2177819	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2229760	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2281792	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2281793	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2377900	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3750747	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3793784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4253038	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4253190	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4253234	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6537540	0.87[ASN][1000 genomes]
rs7081472	0.87[ASN][1000 genomes]
rs7895633	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7898545	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9988727	0.92[AMR][1000 genomes];0.89[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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1917821	ERCC6	cis	parietal	SCAN
rs1917821	ERCC6	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50761600-50770400	Weak transcription	HSMM	muscle
2	chr10:50763400-50768400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:50763400-50771000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:50764400-50769200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:50767000-50770800	Enhancers	Placenta Amnion	Placenta Amnion
6	chr10:50767200-50768600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:50767200-50769200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr10:50767200-50769200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr10:50767200-50769200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr10:50767200-50769400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr10:50767400-50769000	Enhancers	NHDF-Ad	bronchial
12	chr10:50767600-50768400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr10:50767600-50768400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr10:50767600-50768600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr10:50767600-50768600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:50767600-50768800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr10:50768000-50768600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:50768200-50768600	Flanking Active TSS	Osteobl	bone
19	chr10:50768200-50769200	Enhancers	HMEC	breast
20	chr10:50768200-50771200	Weak transcription	HSMMtube	muscle

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