Variant report

Variant	rs4657094
Chromosome Location	chr1:161713826-161713827
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161454426..161456566-chr1:161713079..161714955,2	K562	blood:
2	chr1:161713367..161715023-chr1:161717731..161720555,2	MCF-7	breast:
3	chr1:161708205..161716175-chr1:161716206..161720292,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2340717	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2340719	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2340722	1.00[CEU][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2341472	0.85[AMR][1000 genomes]
rs2490427	0.81[EUR][1000 genomes]
rs2490429	0.83[EUR][1000 genomes]
rs2997506	0.82[EUR][1000 genomes]
rs4233381	0.85[EUR][1000 genomes]
rs4657095	0.82[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4657111	0.81[AMR][1000 genomes]
rs6427628	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6687226	0.85[EUR][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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv1005615	chr1:161707312-161714444	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4657094	DEDD	cis	parietal	SCAN
rs4657094	NTRK1	cis	parietal	SCAN
rs4657094	TIE1	trans	parietal	SCAN
rs4657094	C1orf61	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161706800-161718800	Weak transcription	NH-A	brain
2	chr1:161707600-161719200	Weak transcription	NHLF	lung
3	chr1:161711200-161714200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:161711400-161718800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:161711600-161717600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr1:161711600-161718600	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:161713000-161714000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:161713000-161714200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:161713000-161714600	Enhancers	GM12878-XiMat	blood
10	chr1:161713000-161715400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:161713200-161714000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:161713200-161714000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:161713200-161714400	Enhancers	NHDF-Ad	bronchial
14	chr1:161713200-161715400	Enhancers	K562	blood
15	chr1:161713600-161714000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:161713600-161714000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:161713600-161714000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:161713600-161714000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:161713600-161714000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:161713600-161714000	Enhancers	HMEC	breast
21	chr1:161713600-161714200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:161713600-161714400	Enhancers	Osteobl	bone
23	chr1:161713600-161714600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr1:161713800-161714200	Enhancers	HUVEC	blood vessel
25	chr1:161713800-161714600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links