Variant report

Variant	rs1678199
Chromosome Location	chr2:231345560-231345561
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1102957	0.91[EUR][1000 genomes]
rs1104327	0.92[EUR][1000 genomes]
rs13000851	0.92[EUR][1000 genomes]
rs1615190	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1622822	0.96[AMR][1000 genomes]
rs1622980	0.81[CEU][hapmap];0.94[AMR][1000 genomes]
rs1649876	0.96[EUR][1000 genomes]
rs1649902	0.80[EUR][1000 genomes]
rs1649906	0.92[EUR][1000 genomes]
rs1649907	0.92[EUR][1000 genomes]
rs1649908	0.92[EUR][1000 genomes]
rs1649909	0.88[EUR][1000 genomes]
rs1649910	0.82[EUR][1000 genomes]
rs1649921	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[EUR][1000 genomes]
rs1649925	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1649929	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs1678151	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1678187	0.92[EUR][1000 genomes]
rs1678189	0.90[EUR][1000 genomes]
rs1678190	0.83[EUR][1000 genomes]
rs1678205	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[EUR][1000 genomes]
rs1678210	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1678211	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2195196	0.92[EUR][1000 genomes]
rs2219811	0.93[CEU][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2434050	0.92[EUR][1000 genomes]
rs33078	0.96[EUR][1000 genomes]
rs33079	0.96[EUR][1000 genomes]
rs4972955	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4973324	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4973325	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62195461	0.92[EUR][1000 genomes]
rs6436942	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6436944	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs6436945	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs6717269	0.92[EUR][1000 genomes]
rs6724975	0.92[EUR][1000 genomes]
rs6740016	0.92[EUR][1000 genomes]
rs699660	0.95[EUR][1000 genomes]
rs699661	0.95[EUR][1000 genomes]
rs836232	0.91[EUR][1000 genomes]
rs836236	0.92[EUR][1000 genomes]
rs836237	0.92[EUR][1000 genomes]
rs836238	0.92[EUR][1000 genomes]
rs836239	0.92[EUR][1000 genomes]
rs890668	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv584672	chr2:231289976-231348888	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231288800-231356000	Weak transcription	Stomach Mucosa	stomach
2	chr2:231334200-231356000	Weak transcription	Fetal Intestine Small	intestine
3	chr2:231334800-231358400	Weak transcription	Fetal Stomach	stomach
4	chr2:231335000-231359000	Weak transcription	NHLF	lung
5	chr2:231336000-231356000	Weak transcription	NHDF-Ad	bronchial
6	chr2:231336400-231363400	Weak transcription	Fetal Lung	lung
7	chr2:231336600-231356200	Weak transcription	Placenta	Placenta
8	chr2:231336600-231363400	Weak transcription	Right Ventricle	heart
9	chr2:231336800-231376000	Weak transcription	Colonic Mucosa	Colon
10	chr2:231337800-231351400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:231337800-231359200	Weak transcription	HMEC	breast
12	chr2:231338400-231355200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:231338400-231376200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:231338800-231346200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:231338800-231351800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:231339000-231350800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr2:231339200-231349600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr2:231339200-231354200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:231340000-231347600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:231340000-231358800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:231340600-231349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:231340600-231349200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:231340600-231353800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:231340600-231361000	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:231340800-231345600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:231340800-231349000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:231340800-231351000	Strong transcription	Liver	Liver
28	chr2:231340800-231352800	Strong transcription	Primary B cells from cord blood	blood
29	chr2:231340800-231355600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:231341000-231361000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr2:231341600-231349400	Strong transcription	Left Ventricle	heart
32	chr2:231341600-231349800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr2:231342000-231351200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:231342200-231345600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:231342200-231345600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr2:231342200-231346400	Strong transcription	Adipose Nuclei	Adipose
37	chr2:231342400-231346600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:231343000-231346400	Strong transcription	GM12878-XiMat	blood
39	chr2:231343200-231345800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:231343200-231349400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:231343400-231345600	Strong transcription	HSMM	muscle
42	chr2:231343400-231346600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:231343600-231346000	Strong transcription	Lung	lung
44	chr2:231343800-231345600	Strong transcription	Rectal Smooth Muscle	rectum
45	chr2:231343800-231346200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:231343800-231346600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr2:231343800-231346600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr2:231343800-231347200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:231344000-231345600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:231344000-231345800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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