Variant report

Variant	rs12625600
Chromosome Location	chr20:13702651-13702652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10485767	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap]
rs11696168	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12625704	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs4813143	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap]
rs4814253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6105151	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6105163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6110019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6110023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6110037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6110050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs6514441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7360405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs736365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061303	chr20:13395546-13810990	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916202	chr20:13421724-14043615	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1059817	chr20:13422602-13807968	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1066810	chr20:13451869-14432454	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1061323	chr20:13551004-13746346	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv912689	chr20:13570331-14155881	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv531478	chr20:13580524-13814797	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1059221	chr20:13589432-13977327	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv531479	chr20:13632491-14434432	Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription 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	16 gene(s)	inside rSNPs	diseases
10	esv1793063	chr20:13691562-13708788	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13690600-13706200	Weak transcription	Pancreas	Pancrea
2	chr20:13691800-13706200	Weak transcription	Aorta	Aorta
3	chr20:13691800-13708000	Weak transcription	Fetal Brain Male	brain
4	chr20:13692200-13709200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:13692200-13712200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr20:13692200-13712400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:13692200-13745000	Weak transcription	Small Intestine	intestine
8	chr20:13692400-13712400	Weak transcription	Brain Germinal Matrix	brain
9	chr20:13692400-13717600	Strong transcription	Dnd41	blood
10	chr20:13692800-13712200	Weak transcription	Esophagus	oesophagus
11	chr20:13693000-13721400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr20:13693000-13746400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr20:13693400-13706800	Weak transcription	K562	blood
14	chr20:13694200-13704200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr20:13694400-13748000	Weak transcription	Gastric	stomach
16	chr20:13694600-13764400	Weak transcription	Stomach Mucosa	stomach
17	chr20:13694800-13718200	Weak transcription	Psoas Muscle	Psoas
18	chr20:13695000-13708000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr20:13696000-13715600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr20:13697000-13707600	Weak transcription	HUVEC	blood vessel
21	chr20:13697000-13712400	Weak transcription	Right Ventricle	heart
22	chr20:13697200-13706200	Weak transcription	NHLF	lung
23	chr20:13697200-13706400	Weak transcription	Fetal Kidney	kidney
24	chr20:13697200-13707800	Weak transcription	NHDF-Ad	bronchial
25	chr20:13697200-13708000	Weak transcription	HSMMtube	muscle
26	chr20:13697200-13711600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr20:13697200-13711800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr20:13697200-13711800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr20:13697200-13712400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr20:13697200-13712400	Weak transcription	Brain Angular Gyrus	brain
31	chr20:13697200-13712400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr20:13697200-13712400	Weak transcription	Brain Substantia Nigra	brain
33	chr20:13697200-13712600	Weak transcription	Colon Smooth Muscle	Colon
34	chr20:13697200-13745000	Weak transcription	Colonic Mucosa	Colon
35	chr20:13697400-13711600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr20:13697400-13712400	Weak transcription	NHEK	skin
37	chr20:13697600-13745800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr20:13698000-13705400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr20:13698000-13707800	Weak transcription	Fetal Brain Female	brain
40	chr20:13698000-13709200	Weak transcription	Fetal Intestine Small	intestine
41	chr20:13698000-13712400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr20:13698200-13712400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr20:13698200-13712400	Weak transcription	Spleen	Spleen
44	chr20:13698200-13713000	Weak transcription	Brain Anterior Caudate	brain
45	chr20:13698400-13705400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr20:13698400-13705400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr20:13698400-13705800	Weak transcription	NH-A	brain
48	chr20:13698400-13707800	Weak transcription	Brain Hippocampus Middle	brain
49	chr20:13698400-13708000	Weak transcription	Fetal Lung	lung
50	chr20:13698400-13708000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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