Variant report

Variant	rs4667310
Chromosome Location	chr2:182362843-182362844
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1038034	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10490691	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11553356	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12465604	0.84[LWK][hapmap]
rs12614187	0.93[CEU][hapmap];0.94[CHD][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12619341	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1449259	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16867431	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16867433	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16867437	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16867438	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16867442	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16867443	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16867444	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16867445	0.81[ASN][1000 genomes]
rs1816990	0.86[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290517	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2305581	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2305582	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3770106	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770109	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]
rs3770111	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3770116	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4479393	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4666787	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55890022	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56005177	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56073441	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58662009	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6705247	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67427532	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6756022	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs718449	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72883635	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72883653	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72883655	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72900325	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72900326	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72900343	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7601843	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.83[EUR][1000 genomes];0.83[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4667310	ITGA4	cis	parietal	SCAN
rs4667310	CERKL	cis	parietal	SCAN

Chromatin state (count:57 , 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	chr2:182331400-182363400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:182331400-182382200	Weak transcription	HMEC	breast
5	chr2:182334600-182381400	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:182335000-182366800	Weak transcription	Fetal Stomach	stomach
7	chr2:182335000-182405800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr2:182336800-182382800	Weak transcription	Small Intestine	intestine
9	chr2:182338200-182363400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:182338200-182378400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:182338200-182383400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:182338200-182399400	Weak transcription	Colonic Mucosa	Colon
13	chr2:182338200-182406800	Strong transcription	Fetal Thymus	thymus
14	chr2:182338200-182406800	Weak transcription	Spleen	Spleen
15	chr2:182338400-182382200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:182338600-182405600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr2:182339000-182381000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:182339200-182380600	Strong transcription	Dnd41	blood
19	chr2:182339400-182405600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:182341800-182363400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:182344400-182367200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:182346000-182378600	Weak transcription	Lung	lung
23	chr2:182347200-182399800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:182347400-182363400	Weak transcription	HSMM	muscle
25	chr2:182348200-182377400	Weak transcription	NH-A	brain
26	chr2:182349600-182365000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:182349600-182405800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:182350400-182384600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:182351600-182363400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:182353800-182404200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:182355200-182383000	Strong transcription	GM12878-XiMat	blood
32	chr2:182356000-182406800	Strong transcription	Primary B cells from cord blood	blood
33	chr2:182356200-182379600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:182356400-182367400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr2:182357000-182377800	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr2:182357200-182366800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:182357600-182370800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:182358200-182405800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr2:182359600-182391800	Weak transcription	Adipose Nuclei	Adipose
40	chr2:182361000-182363400	Weak transcription	NHDF-Ad	bronchial
41	chr2:182361000-182363600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:182361000-182365000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:182361000-182376600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:182361200-182363400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:182361200-182363400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:182361600-182363400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:182361600-182363400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:182361800-182398000	Weak transcription	Fetal Intestine Small	intestine
49	chr2:182362000-182363400	Weak transcription	Primary T cells from cord blood	blood
50	chr2:182362000-182363400	Weak transcription	Thymus	Thymus

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