Variant report

Variant	rs6822808
Chromosome Location	chr4:120217365-120217366
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:120216851..120219563-chr4:120219999..120222854,2	K562	blood:
2	chr4:119904231..119906265-chr4:120215953..120218280,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164096	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10003567	0.84[CHB][hapmap]
rs10006259	0.84[CHB][hapmap]
rs10006525	0.84[CHB][hapmap]
rs10006706	0.84[CHB][hapmap]
rs10006877	0.84[CHB][hapmap]
rs10010696	0.81[ASN][1000 genomes]
rs10017335	0.84[CHB][hapmap]
rs10029750	0.83[ASN][1000 genomes]
rs10031033	0.84[CHB][hapmap]
rs10032299	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1011054	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10213342	0.82[ASN][1000 genomes]
rs10518300	0.84[CHB][hapmap]
rs10518328	0.84[CHB][hapmap]
rs1052633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098496	0.83[ASN][1000 genomes]
rs11098497	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098499	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11098501	0.84[CHB][hapmap]
rs11724758	0.94[CHB][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11726229	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs11729521	0.84[CHB][hapmap]
rs11729897	0.82[ASN][1000 genomes]
rs11731571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11732621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732686	0.88[CHB][hapmap]
rs11734241	0.84[CHB][hapmap]
rs11734519	0.82[ASN][1000 genomes]
rs11737400	0.81[EUR][1000 genomes]
rs11931312	0.81[ASN][1000 genomes]
rs11944880	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs12186259	0.90[JPT][hapmap]
rs12501610	0.82[ASN][1000 genomes]
rs12506395	0.83[ASN][1000 genomes]
rs12507565	0.84[CHB][hapmap]
rs12508504	0.84[CHB][hapmap]
rs12511640	0.84[CHB][hapmap]
rs12512517	0.82[ASN][1000 genomes]
rs12513083	0.83[CHB][hapmap]
rs12711071	0.84[CHB][hapmap]
rs13113112	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs13113885	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13114751	0.81[ASN][1000 genomes]
rs13116504	0.84[ASN][1000 genomes]
rs13129661	0.84[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs13133044	0.84[ASN][1000 genomes]
rs13149954	0.81[EUR][1000 genomes]
rs13435802	0.89[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1397608	0.81[ASN][1000 genomes]
rs1480931	0.84[CHB][hapmap]
rs1511015	0.83[ASN][1000 genomes]
rs1511017	0.84[CHB][hapmap]
rs1511018	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1511019	0.89[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1511025	0.84[CHB][hapmap]
rs1546502	0.84[CHB][hapmap]
rs1546503	0.84[CHB][hapmap]
rs1546505	0.84[CHB][hapmap]
rs1551	0.81[ASN][1000 genomes]
rs1980025	0.84[CHB][hapmap]
rs1980026	0.84[CHB][hapmap]
rs2036858	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2175383	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389803	0.84[CHB][hapmap]
rs28374891	0.83[ASN][1000 genomes]
rs28419773	0.83[ASN][1000 genomes]
rs28555550	0.84[ASN][1000 genomes]
rs2892848	0.84[CHB][hapmap]
rs34585914	0.82[ASN][1000 genomes]
rs34616304	0.82[ASN][1000 genomes]
rs34630083	0.82[ASN][1000 genomes]
rs35197422	0.83[ASN][1000 genomes]
rs35271032	0.81[ASN][1000 genomes]
rs35434465	0.83[ASN][1000 genomes]
rs35643470	0.83[ASN][1000 genomes]
rs35916640	0.81[ASN][1000 genomes]
rs3749591	0.89[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs4145951	0.81[ASN][1000 genomes]
rs4833613	0.81[CEU][hapmap]
rs56386062	0.81[ASN][1000 genomes]
rs62320740	0.81[EUR][1000 genomes]
rs6814412	0.83[ASN][1000 genomes]
rs6815725	0.81[ASN][1000 genomes]
rs6834796	0.84[CHB][hapmap]
rs6837898	0.89[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6843509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6848389	0.84[CHB][hapmap]
rs6849561	0.84[CHB][hapmap]
rs6849889	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs714899	0.84[CHB][hapmap]
rs7659194	0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7659403	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7672594	0.84[CHB][hapmap]
rs7684942	0.80[ASN][1000 genomes]
rs7685268	0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs878372	0.84[CHB][hapmap]
rs907205	0.84[CHB][hapmap]
rs9991959	0.84[CHB][hapmap]

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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6822808	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs6822808	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs6822808	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs6822808	RP11-33B1.1	cis	Whole Blood	GTEx
rs6822808	C4orf3	cis	Whole Blood	GTEx
rs6822808	RP11-384K6.6	cis	Whole Blood	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120136200-120219200	Weak transcription	Brain Angular Gyrus	brain
2	chr4:120177000-120220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:120177000-120220200	Weak transcription	Pancreas	Pancrea
4	chr4:120178600-120217600	Weak transcription	Fetal Stomach	stomach
5	chr4:120187000-120219200	Weak transcription	Right Ventricle	heart
6	chr4:120193000-120217600	Weak transcription	Psoas Muscle	Psoas
7	chr4:120193000-120219200	Weak transcription	Fetal Brain Male	brain
8	chr4:120201200-120220200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:120201200-120220200	Weak transcription	Gastric	stomach
10	chr4:120201400-120220200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:120202000-120220200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr4:120206400-120217400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:120206400-120217600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr4:120206400-120217600	Weak transcription	Fetal Intestine Small	intestine
15	chr4:120206400-120218200	Weak transcription	Aorta	Aorta
16	chr4:120206400-120219200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr4:120206400-120219600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:120206400-120219800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:120206400-120219800	Weak transcription	Brain Substantia Nigra	brain
20	chr4:120206400-120220000	Weak transcription	Colonic Mucosa	Colon
21	chr4:120206600-120217600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:120206600-120217600	Weak transcription	Small Intestine	intestine
23	chr4:120206600-120219200	Weak transcription	Hela-S3	cervix
24	chr4:120206600-120219600	Weak transcription	Brain Hippocampus Middle	brain
25	chr4:120206600-120219800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr4:120206600-120220200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:120206800-120217600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr4:120206800-120217600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:120206800-120219200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:120206800-120219200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr4:120206800-120220200	Weak transcription	Stomach Mucosa	stomach
32	chr4:120207000-120217400	Weak transcription	GM12878-XiMat	blood
33	chr4:120207200-120217600	Weak transcription	Colon Smooth Muscle	Colon
34	chr4:120207200-120218200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:120207600-120217800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr4:120207600-120219400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:120207600-120219800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:120207800-120217800	Weak transcription	A549	lung
39	chr4:120208200-120218200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:120208400-120217400	Weak transcription	Fetal Lung	lung
41	chr4:120208400-120219200	Weak transcription	Fetal Heart	heart
42	chr4:120211400-120217600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr4:120211400-120219200	Strong transcription	NHDF-Ad	bronchial
44	chr4:120211600-120217400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:120211600-120219200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr4:120212200-120218000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:120212400-120217800	Weak transcription	K562	blood
48	chr4:120214000-120218000	Weak transcription	Brain Anterior Caudate	brain
49	chr4:120214200-120217600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr4:120214200-120217600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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