Variant report

Variant	rs4972397
Chromosome Location	chr2:174014361-174014362
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:173912619..173914756-chr2:174014173..174017350,3	MCF-7	breast:
2	chr2:174011042..174014620-chr2:174016771..174020819,3	MCF-7	breast:
3	chr2:173944994..173946697-chr2:174012717..174014873,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091428	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11680612	0.95[ASN][1000 genomes]
rs13004345	0.83[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs13009008	0.85[ASN][1000 genomes]
rs13030866	0.90[ASN][1000 genomes]
rs1837470	0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs35109796	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35339538	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3769184	0.88[CHB][hapmap];0.88[JPT][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3769185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4344898	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4972534	0.92[ASN][1000 genomes]
rs6722254	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6750801	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7575189	0.88[CEU][hapmap];0.82[CHB][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs8446	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv834461	chr2:173979734-174038471	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4972397	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174002200-174014600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:174002200-174014600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:174006600-174014400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr2:174007800-174021000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:174007800-174021000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:174008600-174020800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:174012600-174015400	Enhancers	A549	lung
8	chr2:174012800-174014600	Enhancers	Ovary	ovary
9	chr2:174012800-174015200	Enhancers	Fetal Heart	heart
10	chr2:174012800-174015800	Enhancers	Left Ventricle	heart
11	chr2:174012800-174016000	Enhancers	NHEK	skin
12	chr2:174012800-174016200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:174012800-174016600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:174012800-174018000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:174012800-174018400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:174012800-174018400	Enhancers	HMEC	breast
17	chr2:174012800-174018400	Enhancers	Osteobl	bone
18	chr2:174012800-174018600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:174012800-174018600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr2:174012800-174018600	Enhancers	NHDF-Ad	bronchial
21	chr2:174012800-174018600	Enhancers	NHLF	lung
22	chr2:174012800-174020000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:174012800-174026600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr2:174013000-174014600	Enhancers	Stomach Smooth Muscle	stomach
25	chr2:174013000-174016000	Weak transcription	Small Intestine	intestine
26	chr2:174013000-174017600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:174013000-174018000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:174013200-174014400	Enhancers	GM12878-XiMat	blood
29	chr2:174013200-174014400	Weak transcription	HSMM	muscle
30	chr2:174013200-174016000	Enhancers	Right Atrium	heart
31	chr2:174013200-174016400	Enhancers	Psoas Muscle	Psoas
32	chr2:174013200-174017200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:174013200-174018600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:174013400-174025400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:174013600-174015800	Weak transcription	Right Ventricle	heart
36	chr2:174013600-174015800	Weak transcription	HUVEC	blood vessel
37	chr2:174013600-174016400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr2:174013600-174017200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:174013600-174018000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:174013600-174024600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:174013800-174014400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:174013800-174014600	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:174013800-174015000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:174013800-174015200	Weak transcription	NH-A	brain
45	chr2:174014000-174015000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:174014200-174014400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr2:174014200-174015600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links