Variant report

Variant	rs10911121
Chromosome Location	chr1:172124850-172124851
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172113447..172116382-chr1:172123052..172125523,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230630	Chromatin interaction
ENSG00000208024	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10218612	0.85[JPT][hapmap]
rs10442603	0.94[CEU][hapmap]
rs10489730	0.81[JPT][hapmap]
rs10797719	0.81[JPT][hapmap]
rs10797735	0.81[JPT][hapmap]
rs10797791	0.94[CEU][hapmap]
rs10910966	0.81[JPT][hapmap]
rs10911101	0.94[CEU][hapmap]
rs10911109	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10911110	0.94[CEU][hapmap]
rs10911111	0.83[CEU][hapmap]
rs10911112	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10911116	0.94[CEU][hapmap]
rs10911122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911123	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10911124	1.00[CEU][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs10911125	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12047492	0.94[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes]
rs12117047	0.94[EUR][1000 genomes]
rs12120556	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1475230	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1475231	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1555383	0.81[JPT][hapmap]
rs2038481	0.81[JPT][hapmap]
rs2057302	0.81[JPT][hapmap]
rs2146901	0.94[CEU][hapmap]
rs2181624	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2208367	0.81[JPT][hapmap]
rs2295610	0.81[JPT][hapmap]
rs2295611	0.81[JPT][hapmap]
rs2421986	0.81[AMR][1000 genomes]
rs2421987	0.94[CEU][hapmap]
rs35419194	0.98[EUR][1000 genomes]
rs3736791	0.81[JPT][hapmap]
rs4076678	0.81[JPT][hapmap]
rs4604727	0.89[CEU][hapmap]
rs56848769	0.98[EUR][1000 genomes]
rs57543724	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59123063	0.98[EUR][1000 genomes]
rs61046549	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6425599	0.81[JPT][hapmap]
rs6669406	0.81[JPT][hapmap]
rs72719086	0.98[EUR][1000 genomes]
rs7518865	0.81[JPT][hapmap]
rs7530970	0.81[JPT][hapmap]
rs9286842	0.81[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10911121	TNFSF4	cis	parietal	SCAN
rs10911121	TNFSF18	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172114400-172137000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:172115000-172133800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:172115600-172132600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:172119000-172125000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:172122200-172125400	Enhancers	NHEK	skin
6	chr1:172122400-172125000	Weak transcription	Fetal Lung	lung
7	chr1:172123400-172125200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:172123400-172125200	Enhancers	NH-A	brain
9	chr1:172123400-172149200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:172123800-172125000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:172123800-172125200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr1:172123800-172125400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:172123800-172125600	Enhancers	NHLF	lung
14	chr1:172124000-172125000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:172124000-172125000	Weak transcription	Fetal Kidney	kidney
16	chr1:172124000-172125400	Enhancers	NHDF-Ad	bronchial
17	chr1:172124200-172125000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:172124200-172125400	Enhancers	Osteobl	bone
19	chr1:172124800-172125200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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