Variant report

Variant	rs6918561
Chromosome Location	chr6:5669621-5669622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5668378..5671034-chr6:5677672..5680311,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1001568	0.95[CHB][hapmap]
rs1005521	0.80[JPT][hapmap]
rs11243029	0.84[CEU][hapmap]
rs11752777	0.90[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap]
rs12190311	0.89[CEU][hapmap];0.91[MEX][hapmap]
rs12216327	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13213128	0.85[CHB][hapmap]
rs2142738	0.90[CHB][hapmap];0.84[AMR][1000 genomes]
rs2326634	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs4140654	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4959347	0.85[CHB][hapmap]
rs4960125	0.81[CHB][hapmap]
rs6918383	0.89[AMR][1000 genomes]
rs6918675	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6935719	0.86[AMR][1000 genomes]
rs760675	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes]
rs7739358	0.85[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7746913	0.85[CHB][hapmap]
rs877010	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs878988	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9328328	0.94[CHB][hapmap]
rs9378979	0.90[CHB][hapmap];0.85[GIH][hapmap]
rs9378980	0.81[CHB][hapmap]
rs9378983	0.90[CHB][hapmap]
rs9405281	0.85[CHB][hapmap]
rs9405859	0.85[CHB][hapmap];0.82[GIH][hapmap]
rs9502329	0.87[AMR][1000 genomes]
rs9504488	0.85[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][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
rs6918561	NQO2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5641400-5673800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5641600-5671400	Weak transcription	Lung	lung
3	chr6:5642200-5672400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:5650000-5671400	Weak transcription	Small Intestine	intestine
5	chr6:5651200-5671400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:5653200-5677600	Weak transcription	Gastric	stomach
7	chr6:5654600-5671400	Weak transcription	Left Ventricle	heart
8	chr6:5654600-5677600	Weak transcription	Pancreas	Pancrea
9	chr6:5656000-5672200	Weak transcription	Aorta	Aorta
10	chr6:5656800-5669800	Weak transcription	NHEK	skin
11	chr6:5656800-5670000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:5658000-5671400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:5660400-5672600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:5661200-5672200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:5661600-5671400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:5663200-5673400	Weak transcription	Fetal Brain Male	brain
17	chr6:5663400-5672400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr6:5664000-5670200	Enhancers	Primary T cells fromperipheralblood	blood
19	chr6:5664200-5670800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:5664800-5673400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:5665200-5677800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:5665600-5671400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:5665600-5671600	Weak transcription	Spleen	Spleen
24	chr6:5666200-5669800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:5666200-5670600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:5666200-5670800	Enhancers	Fetal Thymus	thymus
27	chr6:5666200-5671400	Weak transcription	GM12878-XiMat	blood
28	chr6:5666200-5673400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:5666600-5670200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:5666800-5670800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr6:5668000-5671000	Weak transcription	Primary B cells from cord blood	blood
32	chr6:5668000-5671400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:5668200-5672400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr6:5668400-5671200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr6:5668400-5671200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:5668400-5671600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:5668400-5672400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr6:5668600-5671200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:5668600-5671200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr6:5668800-5671000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:5668800-5671200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr6:5668800-5671400	Weak transcription	Thymus	Thymus
43	chr6:5668800-5672600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr6:5668800-5672800	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr6:5669400-5670000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:5669400-5674000	Enhancers	Primary T cells from cord blood	blood
47	chr6:5669600-5669800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr6:5669600-5669800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr6:5669600-5671200	Weak transcription	Dnd41	blood

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