Variant report

Variant	rs12188688
Chromosome Location	chr5:179970527-179970528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10069	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10464102	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516143	0.85[JPT][hapmap]
rs10903259	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11249721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11249729	0.86[JPT][hapmap]
rs11249732	0.86[JPT][hapmap]
rs11738044	0.85[JPT][hapmap]
rs11738129	0.84[JPT][hapmap]
rs11738199	0.84[JPT][hapmap]
rs11739089	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11739096	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11742141	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11953441	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11960481	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12054820	0.84[JPT][hapmap]
rs12055052	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187335	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12188182	0.86[JPT][hapmap]
rs13161254	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13164191	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13164854	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13173695	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13177323	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13178018	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188908	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13189165	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13189348	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13190607	0.85[JPT][hapmap]
rs1478360	0.84[JPT][hapmap]
rs2131812	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2387283	0.85[JPT][hapmap]
rs34325776	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34327222	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34524755	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34693772	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34707414	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34753125	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34916144	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35066026	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs36021424	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36028994	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36083585	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6601129	0.84[JPT][hapmap]
rs67209153	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6859296	0.84[JPT][hapmap]
rs6863926	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864038	0.85[JPT][hapmap]
rs6874985	0.84[JPT][hapmap]
rs6876372	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6889526	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6894846	0.86[JPT][hapmap]
rs6896785	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897380	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6897528	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6899301	0.81[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71613470	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7701315	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7704287	0.85[JPT][hapmap]
rs7729397	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
4	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv1031836	chr5:179742033-180676122	Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
6	nsv537984	chr5:179742033-180676122	Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
7	nsv949199	chr5:179743553-180696889	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
8	nsv1023537	chr5:179791679-179982822	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv537985	chr5:179791679-179982822	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS 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	18 gene(s)	inside rSNPs	diseases
10	nsv830564	chr5:179867394-180010096	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	esv1810959	chr5:179945112-179997861	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179950200-179975200	Weak transcription	Psoas Muscle	Psoas
2	chr5:179950200-179984400	Weak transcription	NHDF-Ad	bronchial
3	chr5:179950200-179992000	Weak transcription	Right Ventricle	heart
4	chr5:179950400-179992400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:179950600-180004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:179951000-179991800	Weak transcription	Small Intestine	intestine
7	chr5:179952800-179975400	Weak transcription	Stomach Mucosa	stomach
8	chr5:179953400-179975200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:179953600-179977000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:179953800-179975400	Weak transcription	Fetal Heart	heart
11	chr5:179955600-179977600	Weak transcription	Colonic Mucosa	Colon
12	chr5:179957400-179976800	Weak transcription	Osteobl	bone
13	chr5:179958200-179971000	Weak transcription	HUVEC	blood vessel
14	chr5:179959000-179978200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:179959600-179975200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:179959600-179975400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:179959800-179978600	Weak transcription	Brain Angular Gyrus	brain
18	chr5:179959800-179991600	Weak transcription	HMEC	breast
19	chr5:179960000-179977400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:179960000-180000600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:179960200-179971600	Weak transcription	Brain Substantia Nigra	brain
22	chr5:179960200-179976800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:179960200-179977000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:179960200-179977000	Weak transcription	Brain Anterior Caudate	brain
25	chr5:179960200-179977600	Weak transcription	NHEK	skin
26	chr5:179960200-179982200	Weak transcription	HSMMtube	muscle
27	chr5:179960200-179991600	Weak transcription	Esophagus	oesophagus
28	chr5:179960200-179998200	Weak transcription	Spleen	Spleen
29	chr5:179960400-179991600	Weak transcription	Gastric	stomach
30	chr5:179961000-179977600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:179961200-179976800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr5:179961200-179977800	Weak transcription	Aorta	Aorta
33	chr5:179961200-179992600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:179961400-179974800	Weak transcription	Pancreas	Pancrea
35	chr5:179961400-179977000	Weak transcription	Lung	lung
36	chr5:179961400-179977000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr5:179961400-179991800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:179961600-179971600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr5:179961600-179991800	Weak transcription	Colon Smooth Muscle	Colon
40	chr5:179961800-179982000	Weak transcription	NHLF	lung
41	chr5:179962200-179971800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:179962200-179977600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:179962200-179991800	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:179962600-179975400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:179962600-179982200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:179962800-179977000	Weak transcription	Fetal Brain Male	brain
47	chr5:179964000-179977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr5:179964000-179992600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:179964400-179976800	Weak transcription	Liver	Liver
50	chr5:179964400-179977000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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