Variant report

Variant	rs17075993
Chromosome Location	chr3:43800881-43800882
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:43799834..43802638-chr3:43806373..43808024,2	K562	blood:
2	chr3:43730010..43733179-chr3:43800680..43803701,3	MCF-7	breast:
3	chr3:43800718..43802686-chr3:43808076..43810032,2	K562	blood:
4	chr3:43799880..43802487-chr3:43804101..43806125,2	K562	blood:

Variant related genes	Relation type
ENSG00000011198	Chromatin interaction
ENSG00000160746	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17075984	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9846923	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9879791	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

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	nsv876733	chr3:43768018-43854669	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17075993	WNT1	trans	brain	seeQTL
rs17075993	GPR3	trans	brain	seeQTL
rs17075993	FCER2	trans	brain	seeQTL
rs17075993	ANXA8L2	trans	brain	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43795600-43801200	Enhancers	Primary T cells fromperipheralblood	blood
2	chr3:43797000-43819000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:43797600-43801400	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:43797600-43801800	Enhancers	Fetal Intestine Small	intestine
5	chr3:43797800-43802000	Enhancers	Fetal Intestine Large	intestine
6	chr3:43798000-43801200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr3:43798000-43802000	Enhancers	Placenta	Placenta
8	chr3:43798000-43803800	Enhancers	NHDF-Ad	bronchial
9	chr3:43798800-43801000	Enhancers	Duodenum Mucosa	Duodenum
10	chr3:43798800-43801400	Enhancers	Rectal Mucosa Donor 29	rectum
11	chr3:43798800-43802200	Enhancers	Adipose Nuclei	Adipose
12	chr3:43799000-43801400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:43799000-43801800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:43799000-43802200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr3:43799000-43811600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:43799200-43802000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:43799200-43802000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:43799200-43802000	Enhancers	NHLF	lung
19	chr3:43799200-43802400	Enhancers	HSMM	muscle
20	chr3:43799400-43801200	Enhancers	Spleen	Spleen
21	chr3:43799400-43801400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:43799400-43801400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr3:43799400-43802000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr3:43799400-43802000	Enhancers	Osteobl	bone
25	chr3:43799800-43801000	Enhancers	Colonic Mucosa	Colon
26	chr3:43799800-43801200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:43799800-43801800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:43799800-43802000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:43800000-43801000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr3:43800000-43801200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr3:43800000-43801200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr3:43800000-43801400	Enhancers	Right Ventricle	heart
33	chr3:43800000-43801400	Enhancers	A549	lung
34	chr3:43800000-43801600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr3:43800000-43801800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:43800000-43801800	Enhancers	Fetal Heart	heart
37	chr3:43800000-43802000	Enhancers	HMEC	breast
38	chr3:43800200-43801200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr3:43800200-43801200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr3:43800200-43801200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:43800200-43801400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr3:43800200-43801400	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:43800200-43801600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:43800200-43801600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:43800200-43802000	Enhancers	Right Atrium	heart
46	chr3:43800200-43803000	Enhancers	HUVEC	blood vessel
47	chr3:43800400-43801000	Enhancers	Fetal Muscle Trunk	muscle
48	chr3:43800400-43801200	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:43800400-43801200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:43800400-43801200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links