Variant report

Variant	rs2294698
Chromosome Location	chr6:163995737-163995738
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1047935	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11962088	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs13199835	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13202282	0.83[ASN][1000 genomes]
rs16895015	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs1737324	0.85[JPT][hapmap]
rs1737328	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs17591955	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs1764010	0.85[JPT][hapmap]
rs1764011	0.85[JPT][hapmap]
rs2143358	0.82[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2294703	0.88[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2294706	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2294709	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs35442073	0.83[ASN][1000 genomes]
rs3756879	0.82[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs3763197	0.88[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs41268571	0.82[ASN][1000 genomes]
rs4263561	0.94[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs4709716	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4709717	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4709720	0.88[ASN][1000 genomes]
rs4709722	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6455897	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs6931903	0.88[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs6939218	0.82[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs715020	0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs724826	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7758706	0.88[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs7772756	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs9346960	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap]
rs9347760	0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9364688	0.82[ASN][1000 genomes]
rs9364689	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9364691	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9364692	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018860	chr6:163939347-164532579	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538526	chr6:163939347-164532579	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2758092	chr6:163992064-164161903	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv2759490	chr6:163992064-164161903	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2294698	QKI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163952600-163996600	Weak transcription	Gastric	stomach
2	chr6:163959800-163997200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:163970800-164000200	Weak transcription	Right Atrium	heart
4	chr6:163974000-163997000	Weak transcription	Fetal Intestine Small	intestine
5	chr6:163974200-163997000	Weak transcription	Fetal Intestine Large	intestine
6	chr6:163978000-163998000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr6:163978800-163997600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr6:163979200-163996200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:163980000-163997200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:163980200-163996000	Weak transcription	Small Intestine	intestine
11	chr6:163982800-163996800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr6:163982800-163998000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:163983000-163998400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:163983200-163997400	Weak transcription	Fetal Brain Female	brain
15	chr6:163984800-164000000	Weak transcription	Right Ventricle	heart
16	chr6:163985000-164006800	Weak transcription	Spleen	Spleen
17	chr6:163985800-163996600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr6:163985800-163997600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:163986600-164007000	Weak transcription	Aorta	Aorta
20	chr6:163987600-164007000	Weak transcription	Hela-S3	cervix
21	chr6:163987800-164000200	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:163989600-163997800	Enhancers	Brain Hippocampus Middle	brain
23	chr6:163991200-163996200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:163991200-164001800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr6:163991600-163998200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:163991800-163996000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr6:163992000-163996600	Weak transcription	Fetal Brain Male	brain
28	chr6:163992000-164000000	Strong transcription	HSMM	muscle
29	chr6:163992000-164000600	Weak transcription	Fetal Kidney	kidney
30	chr6:163992200-163996600	Weak transcription	Thymus	Thymus
31	chr6:163992200-163997000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:163992200-163997200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:163992200-164000000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:163992200-164000000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:163992200-164000200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:163992200-164000400	Weak transcription	Pancreas	Pancrea
37	chr6:163992200-164000600	Weak transcription	Fetal Stomach	stomach
38	chr6:163992200-164002000	Weak transcription	Ovary	ovary
39	chr6:163992200-164007200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:163992200-164007200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr6:163992200-164009000	Weak transcription	GM12878-XiMat	blood
42	chr6:163992400-163995800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:163992400-163997400	Weak transcription	Fetal Thymus	thymus
44	chr6:163992400-163997800	Enhancers	Brain Substantia Nigra	brain
45	chr6:163992400-163998200	Weak transcription	Brain Germinal Matrix	brain
46	chr6:163992400-163999000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:163992400-163999200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr6:163992400-163999600	Weak transcription	HSMMtube	muscle
49	chr6:163992400-164000200	Weak transcription	Esophagus	oesophagus
50	chr6:163992400-164001800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links