Variant report

Variant	rs3777487
Chromosome Location	chr6:131584810-131584811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11154621	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11154622	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11754401	1.00[ASN][1000 genomes]
rs11755717	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11758994	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11759793	1.00[ASN][1000 genomes]
rs11759926	1.00[ASN][1000 genomes]
rs1190788	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1190794	1.00[CHB][hapmap]
rs1190799	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1190801	1.00[CHB][hapmap]
rs1190805	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs1190806	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs11961577	1.00[ASN][1000 genomes]
rs1209159	1.00[CHB][hapmap]
rs1317667	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195700	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs13200165	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13205441	1.00[ASN][1000 genomes]
rs13206776	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1322596	0.81[CEU][hapmap];0.93[EUR][1000 genomes]
rs1570348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1729549	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1729558	1.00[CHB][hapmap]
rs1746470	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1746471	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1746473	1.00[CHB][hapmap]
rs17573187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17651753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17787964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs1885641	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2077490	1.00[ASN][1000 genomes]
rs2327102	1.00[ASN][1000 genomes]
rs28360555	1.00[ASN][1000 genomes]
rs34326915	1.00[ASN][1000 genomes]
rs34601891	1.00[ASN][1000 genomes]
rs35017713	1.00[ASN][1000 genomes]
rs35561719	1.00[ASN][1000 genomes]
rs35746376	1.00[ASN][1000 genomes]
rs3777476	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3777489	1.00[ASN][1000 genomes]
rs3777493	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850239	1.00[ASN][1000 genomes]
rs3903759	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4310080	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs4424112	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55893652	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56059672	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56189731	0.98[EUR][1000 genomes]
rs56318353	0.85[EUR][1000 genomes]
rs66533103	1.00[ASN][1000 genomes]
rs67021539	1.00[ASN][1000 genomes]
rs67399092	1.00[ASN][1000 genomes]
rs6937607	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73631985	0.96[EUR][1000 genomes]
rs73634710	0.98[EUR][1000 genomes]
rs749375	1.00[ASN][1000 genomes]
rs7743894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754007	0.98[EUR][1000 genomes]
rs9483238	1.00[ASN][1000 genomes]
rs9492861	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]
rs9492864	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9492865	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9492868	1.00[ASN][1000 genomes]
rs9492869	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9492877	1.00[ASN][1000 genomes]
rs9492880	1.00[ASN][1000 genomes]
rs9492883	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	esv1835599	chr6:131554291-131590766	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv886666	chr6:131573433-131666295	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3777487	VNN3	cis	parietal	SCAN
rs3777487	VNN1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131571800-131587200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:131571800-131591400	Weak transcription	Psoas Muscle	Psoas
3	chr6:131571800-131592600	Weak transcription	Fetal Thymus	thymus
4	chr6:131571800-131596800	Weak transcription	Lung	lung
5	chr6:131571800-131603000	Weak transcription	Esophagus	oesophagus
6	chr6:131571800-131614400	Weak transcription	Gastric	stomach
7	chr6:131572200-131613000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr6:131572600-131587000	Weak transcription	Brain Substantia Nigra	brain
9	chr6:131573000-131590600	Weak transcription	Adipose Nuclei	Adipose
10	chr6:131573400-131591200	Weak transcription	Liver	Liver
11	chr6:131573600-131590400	Weak transcription	Left Ventricle	heart
12	chr6:131573600-131610400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:131573800-131590200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:131574000-131590400	Weak transcription	Brain Anterior Caudate	brain
15	chr6:131574200-131601600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:131574200-131601600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:131574400-131591000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:131575600-131602400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:131577000-131591400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:131577000-131601600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:131577200-131590200	Weak transcription	Fetal Stomach	stomach
22	chr6:131577400-131590400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:131577400-131590400	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:131577400-131590800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:131577400-131601400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:131578800-131590400	Weak transcription	Fetal Lung	lung
27	chr6:131579000-131587400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr6:131579000-131590200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:131579000-131597600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:131579200-131590800	Weak transcription	Fetal Brain Female	brain
31	chr6:131579400-131590400	Weak transcription	Primary B cells from cord blood	blood
32	chr6:131579400-131590600	Weak transcription	Primary T cells from cord blood	blood
33	chr6:131580600-131589600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:131580600-131590200	Weak transcription	Ovary	ovary
35	chr6:131580600-131591200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr6:131580600-131602400	Weak transcription	Small Intestine	intestine
37	chr6:131580600-131602600	Weak transcription	Right Ventricle	heart
38	chr6:131580600-131606000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr6:131580800-131590600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:131580800-131590600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:131580800-131605000	Weak transcription	Fetal Heart	heart
42	chr6:131581000-131590200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:131581200-131587000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr6:131581200-131587200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:131581200-131590200	Weak transcription	Fetal Intestine Large	intestine
46	chr6:131581200-131596600	Weak transcription	Pancreas	Pancrea
47	chr6:131583400-131590800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:131583400-131591800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr6:131583600-131585800	Weak transcription	Fetal Intestine Small	intestine
50	chr6:131583600-131590400	Weak transcription	Primary hematopoietic stem cells	blood

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