Variant report

Variant	rs9492861
Chromosome Location	chr6:131524618-131524619
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11154621	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs11154622	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11754401	0.84[ASN][1000 genomes]
rs11755717	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11758994	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11759793	0.84[ASN][1000 genomes]
rs11759926	0.84[ASN][1000 genomes]
rs1190788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1190794	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1190796	0.91[ASN][1000 genomes]
rs1190799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1190800	0.91[ASN][1000 genomes]
rs1190801	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1190805	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs1190806	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[ASN][1000 genomes]
rs11961577	0.84[ASN][1000 genomes]
rs1209159	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1317667	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13195700	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs13200165	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs13205441	0.84[ASN][1000 genomes]
rs13206776	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs1322596	0.81[CEU][hapmap]
rs1570348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1729549	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1729558	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1746470	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1746471	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1746473	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs1746474	0.91[ASN][1000 genomes]
rs17573187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17651753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17787964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1885641	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs2077490	0.84[ASN][1000 genomes]
rs2327102	0.84[ASN][1000 genomes]
rs28360555	0.84[ASN][1000 genomes]
rs34326915	0.84[ASN][1000 genomes]
rs34601891	0.84[ASN][1000 genomes]
rs35017713	0.84[ASN][1000 genomes]
rs35561719	0.84[ASN][1000 genomes]
rs35746376	0.84[ASN][1000 genomes]
rs3777476	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs3777487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777489	0.84[ASN][1000 genomes]
rs3777493	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3850239	0.84[ASN][1000 genomes]
rs3903759	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4310080	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs4424112	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs56189731	0.84[EUR][1000 genomes]
rs56318353	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66533103	0.84[ASN][1000 genomes]
rs67021539	0.84[ASN][1000 genomes]
rs67399092	0.84[ASN][1000 genomes]
rs6937607	0.84[EUR][1000 genomes]
rs73631985	0.82[EUR][1000 genomes]
rs73634710	0.84[EUR][1000 genomes]
rs749375	0.84[ASN][1000 genomes]
rs7743894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7754007	0.84[EUR][1000 genomes]
rs9483238	0.84[ASN][1000 genomes]
rs9492864	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9492865	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9492868	0.84[ASN][1000 genomes]
rs9492869	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs9492874	0.92[ASN][1000 genomes]
rs9492877	0.84[ASN][1000 genomes]
rs9492880	0.84[ASN][1000 genomes]
rs9492883	1.00[CHB][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv886665	chr6:131518894-131611309	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv830808	chr6:131521115-131735320	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9492861	VNN1	cis	cerebellum	SCAN
rs9492861	VNN3	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131488200-131534800	Weak transcription	Gastric	stomach
2	chr6:131505800-131534600	Weak transcription	Brain Substantia Nigra	brain
3	chr6:131505800-131534800	Weak transcription	Pancreas	Pancrea
4	chr6:131506600-131529800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:131506600-131532000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:131506800-131551800	Weak transcription	Ovary	ovary
7	chr6:131510400-131534800	Weak transcription	Small Intestine	intestine
8	chr6:131513200-131526400	Weak transcription	Fetal Intestine Small	intestine
9	chr6:131513200-131536400	Weak transcription	Esophagus	oesophagus
10	chr6:131514400-131529800	Weak transcription	Brain Germinal Matrix	brain
11	chr6:131514400-131541400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:131518200-131525600	Weak transcription	Fetal Brain Male	brain
13	chr6:131518200-131531800	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:131518800-131534600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:131521000-131534800	Weak transcription	Psoas Muscle	Psoas
16	chr6:131521200-131533000	Weak transcription	Fetal Lung	lung
17	chr6:131521200-131536200	Weak transcription	Lung	lung
18	chr6:131521200-131541400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:131521400-131526400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr6:131521400-131526600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:131521400-131534600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:131521400-131535000	Weak transcription	Left Ventricle	heart
23	chr6:131521600-131525600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr6:131521600-131526200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:131521600-131531400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:131521600-131534600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:131521600-131534800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr6:131521600-131535000	Weak transcription	Aorta	Aorta
29	chr6:131521600-131535200	Weak transcription	Right Ventricle	heart
30	chr6:131521600-131537400	Weak transcription	Adipose Nuclei	Adipose
31	chr6:131521800-131531000	Weak transcription	Liver	Liver
32	chr6:131522000-131526400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr6:131522000-131526600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:131522200-131526200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:131522200-131534600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:131522400-131526600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr6:131522400-131526800	Weak transcription	Brain Anterior Caudate	brain
38	chr6:131522400-131527600	Weak transcription	Primary B cells from cord blood	blood
39	chr6:131522400-131534600	Weak transcription	Brain Hippocampus Middle	brain
40	chr6:131522400-131542200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr6:131522400-131542200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:131522600-131525800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr6:131522600-131531200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:131522600-131531600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:131522600-131533200	Weak transcription	Fetal Stomach	stomach
46	chr6:131522600-131534600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:131522600-131534600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:131522600-131534600	Weak transcription	Fetal Thymus	thymus
49	chr6:131524000-131525000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:131524000-131525400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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