Variant report

Variant	rs3936952
Chromosome Location	chr1:149978552-149978553
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:149857637..149860180-chr1:149975323..149978792,4	K562	blood:
2	chr1:149855536..149863300-chr1:149977462..149985642,29	K562	blood:
3	chr1:149977821..149984701-chr1:150037094..150041280,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178096	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000136631	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10494260	0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11205309	0.94[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11205310	0.83[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12022928	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs12023231	0.83[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap]
rs12023748	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12026500	0.90[ASN][1000 genomes]
rs12082689	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12409885	0.83[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap]
rs16835135	0.85[YRI][hapmap]
rs1868992	0.83[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.87[TSI][hapmap]
rs3738320	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767627	0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3767628	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4926386	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs4926400	0.88[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs58700306	0.83[AMR][1000 genomes]
rs6660842	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72692821	0.85[ASN][1000 genomes]
rs7544531	0.82[ASW][hapmap];0.81[MKK][hapmap];0.85[YRI][hapmap]
rs7551741	0.86[ASN][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	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149948200-149981000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:149948400-149981400	Weak transcription	Esophagus	oesophagus
3	chr1:149952200-149980800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:149953000-149978800	Weak transcription	Pancreas	Pancrea
5	chr1:149957800-149978600	Weak transcription	Spleen	Spleen
6	chr1:149965000-149981400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:149967400-149978600	Weak transcription	Gastric	stomach
8	chr1:149967800-149981200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:149968200-149980800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:149968400-149980800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr1:149968600-149980000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:149969000-149980800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:149969600-149978600	Weak transcription	HepG2	liver
14	chr1:149969600-149978800	Weak transcription	HMEC	breast
15	chr1:149969800-149979000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:149969800-149979800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr1:149969800-149981400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:149970000-149978600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:149970000-149978800	Weak transcription	Small Intestine	intestine
20	chr1:149970000-149980400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:149970000-149981000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:149970000-149981000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:149970000-149981000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:149970200-149980000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:149970200-149980600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:149970400-149978600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:149970400-149979800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:149970600-149980000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:149971600-149978600	Weak transcription	Stomach Mucosa	stomach
30	chr1:149972000-149978800	Weak transcription	NHDF-Ad	bronchial
31	chr1:149972000-149979800	Weak transcription	Left Ventricle	heart
32	chr1:149972200-149980000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:149972600-149979600	Weak transcription	HUVEC	blood vessel
34	chr1:149972800-149981600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr1:149973200-149978600	Enhancers	Brain Substantia Nigra	brain
36	chr1:149973600-149978800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr1:149973800-149978600	Weak transcription	Ovary	ovary
38	chr1:149973800-149978800	Weak transcription	Right Atrium	heart
39	chr1:149973800-149980400	Weak transcription	Aorta	Aorta
40	chr1:149974000-149978600	Weak transcription	Right Ventricle	heart
41	chr1:149974000-149978800	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:149974200-149979000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:149974200-149979000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:149974400-149979000	Strong transcription	Duodenum Mucosa	Duodenum
45	chr1:149974600-149978600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:149974600-149978600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:149974600-149978800	Strong transcription	HSMM	muscle
48	chr1:149974800-149978600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:149974800-149978600	Weak transcription	HSMMtube	muscle
50	chr1:149974800-149979000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links