Variant report

Variant	rs3927201
Chromosome Location	chr2:63001335-63001336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:62931224..62934812-chr2:63000900..63004540,3	K562	blood:
2	chr2:62933389..62934951-chr2:63001020..63002639,2	MCF-7	breast:
3	chr2:63000842..63003590-chr2:63004331..63006276,2	MCF-7	breast:
4	chr2:62682679..62685054-chr2:63000979..63003135,2	MCF-7	breast:
5	chr2:62932469..62934660-chr2:63001228..63003479,2	K562	blood:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10153716	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1022110	0.80[EUR][1000 genomes]
rs11682530	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11688816	0.93[ASN][1000 genomes]
rs12713467	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713468	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12989754	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994674	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13013218	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1420018	0.88[ASN][1000 genomes]
rs1553832	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1828398	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs189671	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1906198	0.81[EUR][1000 genomes]
rs2058566	0.89[ASN][1000 genomes]
rs2136737	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2215870	0.87[ASN][1000 genomes]
rs2430388	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2539980	0.84[ASN][1000 genomes]
rs2539985	0.87[ASN][1000 genomes]
rs2710638	0.88[ASN][1000 genomes]
rs2710640	0.87[ASN][1000 genomes]
rs2710642	0.87[ASN][1000 genomes]
rs34104251	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs360799	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360800	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360801	0.88[ASN][1000 genomes]
rs360804	0.88[ASN][1000 genomes]
rs360807	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4461246	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671050	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671051	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4671450	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545971	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7562149	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7562734	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7573756	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9678329	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9973612	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62958200-63010200	Weak transcription	Primary B cells from cord blood	blood
2	chr2:62961200-63011600	Weak transcription	NHLF	lung
3	chr2:62974200-63017200	Weak transcription	Primary T cells from cord blood	blood
4	chr2:62982200-63009800	Weak transcription	Fetal Intestine Small	intestine
5	chr2:62982200-63033400	Weak transcription	Fetal Intestine Large	intestine
6	chr2:62982400-63006200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:62984400-63009800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:62987800-63001600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:62988000-63009600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:62988000-63010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:62988000-63012400	Weak transcription	HSMM	muscle
12	chr2:62988200-63012400	Weak transcription	HMEC	breast
13	chr2:62991800-63003200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:62992200-63001600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr2:62993400-63001800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:62993400-63007000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:62993600-63004800	Weak transcription	Adipose Nuclei	Adipose
18	chr2:62994400-63001600	Weak transcription	NHDF-Ad	bronchial
19	chr2:62994800-63010200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:62995600-63002000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:62995800-63001600	Weak transcription	Osteobl	bone
22	chr2:62996400-63001600	Weak transcription	NH-A	brain
23	chr2:62997200-63001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:62998200-63001800	Weak transcription	NHEK	skin
25	chr2:62999400-63001400	Genic enhancers	A549	lung
26	chr2:62999600-63002000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:63000200-63001400	Weak transcription	Liver	Liver
28	chr2:63000200-63003400	Genic enhancers	HepG2	liver
29	chr2:63000400-63001400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr2:63000400-63001600	Weak transcription	Colon Smooth Muscle	Colon
31	chr2:63000600-63004000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:63000800-63009200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:63001200-63001800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:63001200-63002000	Enhancers	Ovary	ovary
35	chr2:63001200-63002200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links