Variant report

Variant	rs17177717
Chromosome Location	chr10:50764503-50764504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:50747393..50749498-chr10:50763066..50765045,2	MCF-7	breast:
2	chr10:50756033..50757654-chr10:50761828..50764703,2	K562	blood:

Variant related genes	Relation type
ENSG00000258838	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10857498	0.80[ASN][1000 genomes]
rs10857500	0.80[ASN][1000 genomes]
rs10857512	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10857513	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857514	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10857515	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10857516	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11101137	0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs11101152	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11101167	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11101168	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11101170	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11101171	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11101172	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11101174	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11527805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11594945	0.86[CHB][hapmap]
rs12218602	0.86[CHB][hapmap]
rs12219170	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12220085	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs12259435	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12411620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12413113	0.86[CHB][hapmap]
rs12415597	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1917799	0.86[CHB][hapmap]
rs2222638	0.86[CHB][hapmap]
rs2228528	0.82[CHB][hapmap]
rs2281794	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs3750748	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs3793788	0.82[CHB][hapmap]
rs4253004	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4253013	0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs4253040	0.82[ASN][1000 genomes]
rs4253043	0.95[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.83[ASN][1000 genomes]
rs4253060	0.95[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs4253082	0.81[CHB][hapmap]
rs4253095	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs4253138	0.80[ASN][1000 genomes]
rs4253145	0.80[ASN][1000 genomes]
rs60981594	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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
rs17177717	SLC5A3	trans	brain	seeQTL
rs17177717	DDX6	trans	brain	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50760400-50765600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:50760600-50767400	Weak transcription	HSMMtube	muscle
3	chr10:50761000-50764600	Weak transcription	NHDF-Ad	bronchial
4	chr10:50761600-50765200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:50761600-50770400	Weak transcription	HSMM	muscle
6	chr10:50761800-50764600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr10:50761800-50764600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr10:50762400-50764600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr10:50763400-50764600	Weak transcription	HMEC	breast
10	chr10:50763400-50768400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:50763400-50771000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:50764400-50765600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr10:50764400-50766800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr10:50764400-50768200	Enhancers	Osteobl	bone
15	chr10:50764400-50769200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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