Variant report

Variant	rs3770109
Chromosome Location	chr2:182388628-182388629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1038034	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10490691	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11553356	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12614187	0.93[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12619341	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12623687	0.80[ASN][1000 genomes]
rs12623737	0.80[ASN][1000 genomes]
rs1449259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16867431	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16867433	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16867437	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16867438	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16867442	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16867443	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16867444	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16867445	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1816990	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2290517	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305582	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770116	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4479393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4666787	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667310	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55741565	0.80[ASN][1000 genomes]
rs55890022	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56005177	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56073441	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56081507	0.80[ASN][1000 genomes]
rs56104379	0.80[ASN][1000 genomes]
rs56263562	0.80[ASN][1000 genomes]
rs58018201	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58662009	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6705247	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67427532	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6756022	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs718449	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72883635	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72883653	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72883655	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72883670	0.80[ASN][1000 genomes]
rs72883678	0.80[ASN][1000 genomes]
rs72883679	0.80[ASN][1000 genomes]
rs72883681	0.80[ASN][1000 genomes]
rs72900325	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72900326	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72900343	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7601843	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs971741	0.80[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	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1002647	chr2:182078521-182392273	Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv536064	chr2:182078521-182392273	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1014910	chr2:182375267-182544114	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv536065	chr2:182375267-182544114	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3770109	ITGA4	cis	parietal	SCAN
rs3770109	CERKL	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182324400-182410400	Weak transcription	NHLF	lung
2	chr2:182330000-182390200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:182335000-182405800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr2:182338200-182399400	Weak transcription	Colonic Mucosa	Colon
5	chr2:182338200-182406800	Strong transcription	Fetal Thymus	thymus
6	chr2:182338200-182406800	Weak transcription	Spleen	Spleen
7	chr2:182338600-182405600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:182339400-182405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:182347200-182399800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:182349600-182405800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr2:182353800-182404200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:182356000-182406800	Strong transcription	Primary B cells from cord blood	blood
13	chr2:182358200-182405800	Strong transcription	Primary hematopoietic stem cells	blood
14	chr2:182359600-182391800	Weak transcription	Adipose Nuclei	Adipose
15	chr2:182361800-182398000	Weak transcription	Fetal Intestine Small	intestine
16	chr2:182364000-182399200	Weak transcription	HSMM	muscle
17	chr2:182366200-182390200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:182366400-182399600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:182377200-182396800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:182378200-182390800	Weak transcription	NH-A	brain
21	chr2:182378800-182389800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:182380200-182390000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:182380600-182390400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:182381200-182397800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:182381600-182389400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:182382600-182405600	Strong transcription	Dnd41	blood
27	chr2:182382800-182406200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:182383000-182390000	Weak transcription	Left Ventricle	heart
29	chr2:182383000-182404600	Weak transcription	Esophagus	oesophagus
30	chr2:182383000-182405800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr2:182383000-182406000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:182383400-182404600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:182383600-182405600	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr2:182383600-182405600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:182384200-182389200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:182384200-182406000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr2:182384200-182406400	Strong transcription	Primary T cells from cord blood	blood
38	chr2:182384600-182388800	Strong transcription	Thymus	Thymus
39	chr2:182384600-182397200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:182385200-182389800	Weak transcription	Aorta	Aorta
41	chr2:182385200-182390200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:182385600-182389800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:182386000-182404600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:182386200-182395600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
45	chr2:182386200-182395800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:182386200-182396800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr2:182386200-182396800	Strong transcription	GM12878-XiMat	blood
48	chr2:182386200-182402800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr2:182386400-182395600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr2:182387000-182403400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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