Variant report

Variant	rs2345873
Chromosome Location	chr2:153248404-153248405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10432492	0.81[MEX][hapmap]
rs10497101	0.83[CHD][hapmap]
rs10931069	0.85[CHD][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap]
rs11674872	0.81[MEX][hapmap]
rs12478426	0.81[MEX][hapmap]
rs13029771	0.85[CHD][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap]
rs13386403	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs13391023	0.82[CEU][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13396439	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13397890	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13402243	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13405110	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13405868	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414887	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13418748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419000	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427076	0.82[CEU][hapmap]
rs13428569	0.91[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs13430448	0.91[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs16831028	0.83[CHD][hapmap];0.90[MEX][hapmap]
rs16831068	0.81[CHD][hapmap]
rs2345903	0.81[CHD][hapmap];0.90[MEX][hapmap]
rs3811577	0.91[CEU][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3890370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4425036	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4664103	0.82[CHD][hapmap];0.90[MEX][hapmap]
rs4664106	0.84[CHD][hapmap];0.90[MEX][hapmap]
rs56095564	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61292193	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62180766	0.94[ASN][1000 genomes]
rs6704965	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs6715843	0.82[CHD][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap]
rs6725656	0.83[JPT][hapmap]
rs6725789	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs6754501	0.83[JPT][hapmap]
rs6761815	0.91[CEU][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs73967855	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73967856	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73967858	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73967990	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1005012	chr2:153206764-153273886	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153226200-153249400	Weak transcription	Right Ventricle	heart
2	chr2:153226200-153251800	Weak transcription	HSMMtube	muscle
3	chr2:153229200-153252400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:153233400-153249000	Weak transcription	Gastric	stomach
5	chr2:153233800-153255400	Weak transcription	NHEK	skin
6	chr2:153237400-153249000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:153237400-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:153237400-153255400	Weak transcription	HMEC	breast
9	chr2:153238600-153258600	Weak transcription	Left Ventricle	heart
10	chr2:153241200-153251600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:153241200-153255400	Weak transcription	Pancreas	Pancrea
12	chr2:153241600-153249000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:153242800-153249200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:153242800-153252600	Weak transcription	A549	lung
15	chr2:153243000-153251600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:153243200-153249200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:153243400-153252600	Weak transcription	Fetal Brain Female	brain
18	chr2:153243800-153252000	Weak transcription	Fetal Lung	lung
19	chr2:153245000-153249200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:153245000-153251800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:153245800-153250800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:153245800-153250800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:153246000-153251400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:153246400-153251600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:153246600-153266600	Enhancers	Brain Substantia Nigra	brain
26	chr2:153247000-153249000	Enhancers	Brain Hippocampus Middle	brain
27	chr2:153247000-153251800	Enhancers	Brain Anterior Caudate	brain
28	chr2:153247000-153257800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:153247200-153255400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr2:153247400-153249000	Weak transcription	Lung	lung
31	chr2:153247400-153249400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:153247400-153250800	Enhancers	Brain Angular Gyrus	brain
33	chr2:153247400-153251600	Weak transcription	Ovary	ovary
34	chr2:153247400-153252600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:153247400-153252600	Weak transcription	Fetal Stomach	stomach
36	chr2:153247400-153255400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:153247400-153277600	Weak transcription	Fetal Intestine Small	intestine
38	chr2:153247800-153249400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:153247800-153251400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:153247800-153258800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:153248000-153249200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:153248000-153249400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr2:153248000-153250000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:153248000-153250800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:153248000-153251400	Weak transcription	Fetal Brain Male	brain
46	chr2:153248200-153249000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:153248200-153249200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:153248200-153249400	Weak transcription	HepG2	liver
49	chr2:153248200-153251200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:153248200-153251600	Weak transcription	Psoas Muscle	Psoas

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