Variant report

Variant	rs2305401
Chromosome Location	chr3:160227606-160227607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10513550	1.00[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11920289	0.86[EUR][1000 genomes]
rs12233589	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs2275153	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2305406	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33999879	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773371	1.00[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3806629	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272959	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55815116	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56119270	0.86[EUR][1000 genomes]
rs56124988	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56150006	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56343019	1.00[ASN][1000 genomes]
rs56396435	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56401539	0.93[EUR][1000 genomes]
rs57030267	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57050097	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57277659	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57285344	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57328745	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57555307	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58377812	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58627305	0.86[EUR][1000 genomes]
rs58654032	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58776572	0.93[EUR][1000 genomes]
rs58915028	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59695030	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59799252	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60066272	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60153357	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60222090	0.83[ASN][1000 genomes]
rs60517889	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60607858	0.93[EUR][1000 genomes]
rs60914777	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61066536	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272169	0.83[ASN][1000 genomes]
rs62272171	0.84[AMR][1000 genomes]
rs62272176	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272179	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272180	0.86[EUR][1000 genomes]
rs62272181	0.87[EUR][1000 genomes]
rs62272185	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272187	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272188	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272190	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272191	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272193	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272196	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272197	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272198	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272207	0.86[EUR][1000 genomes]
rs62272231	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272236	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272237	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272243	0.84[AMR][1000 genomes]
rs62272245	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272247	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62272249	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62272251	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62272253	0.84[AMR][1000 genomes]
rs62272254	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272255	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272256	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272257	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272258	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272259	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62272780	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272781	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272785	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272790	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272793	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272799	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62272804	1.00[ASN][1000 genomes]
rs62272805	1.00[ASN][1000 genomes]
rs62272806	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272831	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272833	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272836	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272838	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66769612	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66850724	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67403526	0.95[ASN][1000 genomes]
rs68069205	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73154564	0.84[AMR][1000 genomes]
rs73154582	0.92[AMR][1000 genomes]
rs73154587	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73155914	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614701	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs7618017	0.87[EUR][1000 genomes]
rs7645798	0.89[EUR][1000 genomes]
rs7648832	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9637414	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	esv1797113	chr3:160217483-160245980	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv877700	chr3:160223172-160248363	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160204000-160238200	Weak transcription	Small Intestine	intestine
2	chr3:160213000-160228600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:160215600-160228200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:160215600-160254200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:160215800-160227800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:160215800-160227800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:160215800-160227800	Strong transcription	NHDF-Ad	bronchial
8	chr3:160215800-160228200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:160215800-160254000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:160215800-160254200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:160215800-160254200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:160216000-160227800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:160216000-160227800	Strong transcription	Placenta	Placenta
14	chr3:160216000-160228000	Strong transcription	Duodenum Mucosa	Duodenum
15	chr3:160216000-160254200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr3:160216200-160227800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:160216200-160227800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:160216200-160227800	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:160216200-160227800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:160216200-160227800	Strong transcription	Adipose Nuclei	Adipose
21	chr3:160216200-160228600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:160216200-160249200	Strong transcription	Liver	Liver
23	chr3:160216200-160254200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:160216400-160228200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr3:160216400-160228800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:160216400-160254400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:160216800-160253800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:160217000-160227800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:160217200-160254000	Strong transcription	Dnd41	blood
30	chr3:160217400-160227800	Strong transcription	HSMM	muscle
31	chr3:160217400-160228000	Strong transcription	Osteobl	bone
32	chr3:160217400-160259600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr3:160217600-160227800	Strong transcription	NH-A	brain
34	chr3:160217800-160235000	Weak transcription	Fetal Brain Male	brain
35	chr3:160218200-160227800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:160218200-160228400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:160218400-160227800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr3:160218400-160227800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:160218600-160227800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:160218600-160228000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr3:160218800-160244800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:160219000-160227800	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:160219600-160233400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:160219800-160242200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:160219800-160263600	Weak transcription	Right Ventricle	heart
46	chr3:160220600-160246200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:160220600-160261200	Weak transcription	Pancreas	Pancrea
48	chr3:160220800-160232600	Weak transcription	Aorta	Aorta
49	chr3:160221600-160249000	Strong transcription	HUVEC	blood vessel
50	chr3:160222000-160230400	Weak transcription	HSMMtube	muscle

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