Variant report

Variant	rs638274
Chromosome Location	chr3:159741259-159741260
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RXRA	chr3:159741165-159741641	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:159739668..159742959-chr3:159743211..159746773,4	MCF-7	breast:

Variant related genes	Relation type
LINC01100	TF binding region
ENSG00000242107	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13061089	0.93[EUR][1000 genomes]
rs1651079	0.90[EUR][1000 genomes]
rs1651080	0.86[EUR][1000 genomes]
rs2279741	0.87[YRI][hapmap]
rs2279742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2647926	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2647927	0.84[EUR][1000 genomes]
rs2647938	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs2914117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914118	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2914119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2936298	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2936300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936301	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679868	0.86[YRI][hapmap]
rs505190	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs507822	0.95[EUR][1000 genomes]
rs507927	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589017	0.86[EUR][1000 genomes]
rs600614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635602	0.87[EUR][1000 genomes]
rs6441286	0.86[YRI][hapmap]
rs659596	0.83[EUR][1000 genomes]
rs670705	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6778021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829769	chr3:159606913-159805282	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv1806743	chr3:159723529-159744022	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159739000-159741400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr3:159739000-159742000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:159740600-159742200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:159740800-159741600	Enhancers	NHLF	lung
5	chr3:159740800-159741800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:159740800-159742200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:159740800-159742200	Enhancers	NHDF-Ad	bronchial
8	chr3:159741000-159741600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:159741000-159741600	Enhancers	HMEC	breast
10	chr3:159741000-159741600	Enhancers	NH-A	brain
11	chr3:159741200-159744000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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