Variant report

Variant	rs2029361
Chromosome Location	chr3:160209895-160209896
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160195689..160198943-chr3:160208326..160210743,3	K562	blood:
2	chr3:160209467..160214464-chr3:160215473..160219309,5	K562	blood:
3	chr3:160166051..160168195-chr3:160209216..160211135,2	MCF-7	breast:
4	chr3:160209082..160210967-chr3:160217809..160219865,2	K562	blood:

Variant related genes	Relation type
ENSG00000213186	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1141023	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236389	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236452	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17236487	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17826161	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1882124	0.87[ASN][1000 genomes]
rs1882128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1920645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1920648	0.87[ASN][1000 genomes]
rs1920654	0.87[ASN][1000 genomes]
rs1979160	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2152424	0.88[ASN][1000 genomes]
rs2272489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35281166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3737214	0.88[ASN][1000 genomes]
rs41272955	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41272957	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4254702	0.88[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4434183	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679883	0.94[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680577	0.88[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680582	0.88[CEU][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55853078	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55930449	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56030166	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56051094	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56322040	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6776582	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780828	0.87[ASN][1000 genomes]
rs6806971	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154549	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73154552	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154567	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73154591	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154596	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154600	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73154602	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155903	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73155920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73155924	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622031	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826290	0.96[ASN][1000 genomes]
rs9845172	0.87[ASN][1000 genomes]
rs9847144	0.87[ASN][1000 genomes]
rs9876980	0.87[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160193400-160213000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:160199000-160211600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:160204000-160211200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:160204000-160215800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:160204000-160216000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:160204000-160219000	Weak transcription	Lung	lung
7	chr3:160204000-160219000	Weak transcription	Thymus	Thymus
8	chr3:160204000-160224000	Weak transcription	Gastric	stomach
9	chr3:160204000-160238200	Weak transcription	Small Intestine	intestine
10	chr3:160204200-160213200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:160204200-160215600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:160204200-160215800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:160204200-160215800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:160204200-160215800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:160204200-160215800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr3:160204200-160215800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:160204200-160215800	Weak transcription	Fetal Thymus	thymus
18	chr3:160204200-160215800	Weak transcription	HSMM	muscle
19	chr3:160204200-160215800	Weak transcription	NHDF-Ad	bronchial
20	chr3:160204200-160216000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:160204200-160216000	Weak transcription	Osteobl	bone
22	chr3:160204200-160216200	Weak transcription	Primary T cells from cord blood	blood
23	chr3:160204200-160216200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:160204200-160216200	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:160204200-160216200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:160204200-160216200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:160204200-160216200	Weak transcription	Liver	Liver
28	chr3:160204200-160216200	Weak transcription	HMEC	breast
29	chr3:160204200-160216400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr3:160204200-160216400	Weak transcription	HUVEC	blood vessel
31	chr3:160204200-160216800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:160204200-160217200	Weak transcription	Colon Smooth Muscle	Colon
33	chr3:160204200-160217600	Weak transcription	NH-A	brain
34	chr3:160204200-160218800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr3:160204200-160218800	Weak transcription	Fetal Intestine Large	intestine
36	chr3:160204200-160219000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:160204200-160219000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:160204200-160219000	Weak transcription	NHEK	skin
39	chr3:160204200-160219200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:160204200-160219200	Weak transcription	Aorta	Aorta
41	chr3:160204200-160219200	Weak transcription	Left Ventricle	heart
42	chr3:160204200-160219400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:160204200-160224400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:160204200-160224800	Weak transcription	GM12878-XiMat	blood
45	chr3:160204200-160225400	Weak transcription	Fetal Kidney	kidney
46	chr3:160204400-160215600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:160204400-160215800	Weak transcription	Primary B cells from cord blood	blood
48	chr3:160204400-160216400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:160209200-160218600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:160209200-160219200	Weak transcription	Fetal Stomach	stomach

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