Variant report

Variant	rs12162306
Chromosome Location	chr2:39589288-39589289
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1012689	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10169329	0.82[AFR][1000 genomes]
rs10185961	0.85[EUR][1000 genomes]
rs10193807	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10196447	0.87[AFR][1000 genomes]
rs10197632	0.85[AFR][1000 genomes]
rs10199948	0.87[AFR][1000 genomes]
rs10865148	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10865151	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs11124671	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11124672	0.85[AFR][1000 genomes]
rs11124674	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11124675	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11124678	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11124680	0.82[ASN][1000 genomes]
rs11677383	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11677611	0.85[ASN][1000 genomes]
rs11688033	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11688352	0.85[ASN][1000 genomes]
rs12151392	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12618944	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12624242	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712634	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12712640	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12712642	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12712643	0.84[ASN][1000 genomes]
rs12997072	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13015356	0.81[EUR][1000 genomes]
rs13405577	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1861733	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1861734	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2024514	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2058863	0.93[AFR][1000 genomes]
rs2302749	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2373528	0.83[EUR][1000 genomes]
rs2888593	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3732053	0.85[AMR][1000 genomes]
rs3755171	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3755172	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3755176	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3770662	0.82[ASN][1000 genomes]
rs3770664	0.82[ASN][1000 genomes]
rs3770671	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770672	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770673	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770674	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4488638	0.83[EUR][1000 genomes]
rs6544214	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6544215	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6544216	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6709424	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6714566	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6719469	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6753014	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7340455	0.95[ASN][1000 genomes]
rs7421175	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7425616	0.80[AMR][1000 genomes]
rs7561630	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7569037	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7569492	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7573923	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7581692	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7582848	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7594145	0.91[ASN][1000 genomes]
rs7595469	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7596222	0.84[AFR][1000 genomes]
rs7597300	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7605427	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7608958	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9037	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9309036	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9309037	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9309038	0.93[AFR][1000 genomes]
rs9309039	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
11	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv873887	chr2:39468676-39601889	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39572200-39597600	Weak transcription	Osteobl	bone
2	chr2:39584400-39598400	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:39584400-39604600	Weak transcription	Right Ventricle	heart
4	chr2:39584800-39591600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:39585000-39591400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:39585200-39590600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
7	chr2:39585200-39590600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
8	chr2:39585200-39591400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
9	chr2:39585400-39590200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
10	chr2:39585600-39591600	Weak transcription	Fetal Heart	heart
11	chr2:39586000-39590800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
12	chr2:39586800-39590400	Weak transcription	Left Ventricle	heart
13	chr2:39587000-39589800	Weak transcription	HSMMtube	muscle
14	chr2:39587000-39596800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:39587000-39597000	Weak transcription	NHLF	lung
16	chr2:39587000-39608800	Weak transcription	Pancreas	Pancrea
17	chr2:39587200-39590000	Weak transcription	HSMM	muscle
18	chr2:39587200-39604400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:39587800-39594400	Weak transcription	Stomach Mucosa	stomach
20	chr2:39587800-39604800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr2:39588000-39589600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:39588000-39589800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:39588000-39590000	Weak transcription	Fetal Stomach	stomach
24	chr2:39588000-39595400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:39588000-39607800	Weak transcription	Ovary	ovary
26	chr2:39588000-39608800	Weak transcription	Lung	lung
27	chr2:39588000-39609000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
29	chr2:39588200-39589400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:39588200-39589600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr2:39588200-39589600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:39588200-39589600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:39588200-39589800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr2:39588200-39590000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:39588200-39590400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:39588200-39591200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:39588200-39599800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:39588200-39602800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:39588200-39603000	Weak transcription	Adipose Nuclei	Adipose
40	chr2:39588400-39589800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:39588400-39589800	Weak transcription	Fetal Lung	lung
42	chr2:39588400-39596800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:39588400-39603000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:39588600-39599400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:39589200-39590600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
46	chr2:39589200-39590600	ZNF genes & repeats	HepG2	liver
47	chr2:39589200-39591600	ZNF genes & repeats	A549	lung

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