Variant report

Variant	rs7304518
Chromosome Location	chr12:4257018-4257019
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10459129	0.85[EUR][1000 genomes]
rs10744631	0.83[EUR][1000 genomes]
rs10774198	0.98[EUR][1000 genomes]
rs10848983	0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs10848984	0.87[ASN][1000 genomes]
rs10848986	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10848988	0.99[EUR][1000 genomes]
rs11063004	0.87[ASN][1000 genomes]
rs11063007	0.86[ASN][1000 genomes]
rs11063008	0.86[ASN][1000 genomes]
rs11063009	0.83[ASN][1000 genomes]
rs11063011	0.83[EUR][1000 genomes]
rs11063012	0.85[EUR][1000 genomes]
rs11063013	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12228949	0.82[ASN][1000 genomes]
rs12229320	0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs12579541	0.87[ASN][1000 genomes]
rs12579556	0.87[ASN][1000 genomes]
rs1861175	1.00[EUR][1000 genomes]
rs1978311	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2110592	0.87[ASN][1000 genomes]
rs2160160	0.87[ASN][1000 genomes]
rs2358836	0.87[ASN][1000 genomes]
rs4766207	0.81[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4766208	0.87[ASN][1000 genomes]
rs4766211	0.87[ASN][1000 genomes]
rs6489519	0.83[EUR][1000 genomes]
rs7137733	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7298905	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs759306	0.87[ASN][1000 genomes]
rs759310	0.95[EUR][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	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1050474	chr12:4226760-4389238	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7304518	CD4	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4246800-4257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:4252400-4262600	Weak transcription	Esophagus	oesophagus
3	chr12:4252400-4262600	Weak transcription	Lung	lung
4	chr12:4252600-4257600	Weak transcription	Colonic Mucosa	Colon
5	chr12:4252600-4257600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr12:4252600-4258200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr12:4252600-4258400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:4252600-4258400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:4252800-4257400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:4252800-4258400	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:4252800-4258400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr12:4253200-4257400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:4254400-4258400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:4254600-4259400	Enhancers	Primary B cells from cord blood	blood
15	chr12:4254800-4264400	Enhancers	Primary B cells from peripheral blood	blood
16	chr12:4255000-4258400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:4255200-4257200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr12:4255200-4258200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:4255200-4258600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:4255400-4257200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:4255400-4258000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr12:4255600-4257200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr12:4255600-4257600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:4255600-4257600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:4255800-4257600	Weak transcription	HMEC	breast
26	chr12:4255800-4257600	Weak transcription	NHEK	skin
27	chr12:4255800-4257800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:4255800-4258200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:4256000-4257400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr12:4256000-4258400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:4256200-4257800	Enhancers	Primary hematopoietic stem cells	blood
32	chr12:4256200-4258400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:4256400-4257200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr12:4256400-4258000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:4256600-4257600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:4256600-4257600	Weak transcription	Small Intestine	intestine
37	chr12:4256600-4257600	Weak transcription	Spleen	Spleen
38	chr12:4256600-4258200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:4256800-4257600	Weak transcription	Fetal Thymus	thymus
40	chr12:4256800-4258600	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr12:4256800-4261000	Weak transcription	K562	blood
42	chr12:4256800-4265400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr12:4257000-4258000	Enhancers	GM12878-XiMat	blood
44	chr12:4257000-4258200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:4257000-4262800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr12:4257000-4265400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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