Variant report

Variant	rs12190311
Chromosome Location	chr6:5665387-5665388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11243029	0.89[CEU][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12174223	1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12216327	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12662009	0.89[ASN][1000 genomes]
rs13213128	0.84[JPT][hapmap]
rs3812177	0.95[ASN][1000 genomes]
rs3828857	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs4140654	0.81[CEU][hapmap]
rs4959347	0.84[JPT][hapmap]
rs6918561	0.89[CEU][hapmap];0.91[MEX][hapmap]
rs760675	0.81[CEU][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap]
rs7739358	0.80[CEU][hapmap];0.83[JPT][hapmap]
rs7746913	0.84[JPT][hapmap]

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	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12190311	NQO2	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5641400-5665400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:5641400-5673800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:5641600-5665400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:5641600-5671400	Weak transcription	Lung	lung
5	chr6:5642200-5672400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:5645400-5666200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:5650000-5671400	Weak transcription	Small Intestine	intestine
8	chr6:5651200-5671400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:5653200-5677600	Weak transcription	Gastric	stomach
10	chr6:5654600-5671400	Weak transcription	Left Ventricle	heart
11	chr6:5654600-5677600	Weak transcription	Pancreas	Pancrea
12	chr6:5656000-5672200	Weak transcription	Aorta	Aorta
13	chr6:5656800-5669800	Weak transcription	NHEK	skin
14	chr6:5656800-5670000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:5658000-5671400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:5660400-5672600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:5661200-5672200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:5661400-5665400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:5661400-5666000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:5661600-5671400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:5662600-5666200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr6:5663200-5673400	Weak transcription	Fetal Brain Male	brain
23	chr6:5663400-5666200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:5663400-5672400	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr6:5663600-5665600	Enhancers	Primary T cells from cord blood	blood
26	chr6:5663600-5667200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr6:5663600-5668200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr6:5663800-5665400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr6:5663800-5665800	Enhancers	Fetal Thymus	thymus
30	chr6:5664000-5665600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr6:5664000-5668000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr6:5664000-5668200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr6:5664000-5670200	Enhancers	Primary T cells fromperipheralblood	blood
34	chr6:5664200-5666200	Enhancers	GM12878-XiMat	blood
35	chr6:5664200-5666800	Enhancers	Primary B cells from peripheral blood	blood
36	chr6:5664200-5670800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:5664400-5665400	Weak transcription	Fetal Stomach	stomach
38	chr6:5664400-5665800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:5664400-5666800	Enhancers	Thymus	Thymus
40	chr6:5664400-5668600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr6:5664600-5665400	Weak transcription	Spleen	Spleen
42	chr6:5664600-5668800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:5664800-5665600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:5664800-5667000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:5664800-5669600	Enhancers	Dnd41	blood
46	chr6:5664800-5673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:5665000-5665800	Enhancers	Primary B cells from cord blood	blood
48	chr6:5665200-5668600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:5665200-5677800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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