Variant report

Variant	rs2116704
Chromosome Location	chr12:31566003-31566004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1012154	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs10743757	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10743758	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs10743759	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10771827	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10771828	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10771838	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10771843	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10771844	0.85[EUR][1000 genomes]
rs10771845	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10771846	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843942	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10843947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10843958	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10843959	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10843963	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11051435	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051437	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051439	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11051441	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1150942	0.86[CHB][hapmap]
rs1150953	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1150954	0.86[CHB][hapmap]
rs1150955	0.86[CHB][hapmap]
rs11615961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259235	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1259236	0.85[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs1259356	0.86[CHB][hapmap]
rs1259359	0.86[CHB][hapmap]
rs1259386	0.83[CHB][hapmap]
rs1259409	0.86[CHB][hapmap]
rs1259428	0.92[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1259432	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs1259437	0.86[CHB][hapmap]
rs1272773	0.86[CHB][hapmap]
rs1469673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1677189	0.86[CHB][hapmap]
rs1716216	0.93[CHB][hapmap]
rs1996693	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2352048	0.83[EUR][1000 genomes]
rs2568884	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2617190	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2617191	0.86[CHB][hapmap]
rs2617200	0.93[CHB][hapmap];0.90[JPT][hapmap]
rs2682697	0.83[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682700	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2888762	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35906870	0.80[AMR][1000 genomes]
rs3803113	0.83[EUR][1000 genomes]
rs3844573	0.89[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3850965	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3898368	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4482118	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4930980	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4931488	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931501	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4931506	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4931507	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6416254	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6487989	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6487992	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66521153	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs708200	0.81[AMR][1000 genomes]
rs708209	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs708212	0.80[CHB][hapmap]
rs708214	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs708217	0.80[CHB][hapmap]
rs708219	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7133082	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7134365	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7135856	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7136476	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7136943	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7137406	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71440988	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7294574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7302698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7303447	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7303848	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7307593	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7307616	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7313118	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7313158	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7313689	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7314417	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs793146	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs793150	0.80[CHB][hapmap]
rs793154	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793157	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793158	0.80[CHB][hapmap]
rs793174	0.86[CHB][hapmap]
rs793176	0.93[CHB][hapmap]
rs793177	0.86[CHB][hapmap]
rs793180	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs793184	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793186	0.86[CHB][hapmap]
rs7954023	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7954595	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7957026	1.00[CEU][hapmap]
rs7959877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7962896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7963161	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7967832	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7968291	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7974437	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7975761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7976644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7977453	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs899159	0.82[CEU][hapmap];0.86[CHB][hapmap]
rs9738834	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31536400-31624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:31536600-31577400	Weak transcription	Small Intestine	intestine
3	chr12:31537400-31604800	Weak transcription	Spleen	Spleen
4	chr12:31537600-31580800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:31537800-31572400	Weak transcription	Stomach Mucosa	stomach
6	chr12:31539800-31584800	Weak transcription	Fetal Heart	heart
7	chr12:31540800-31572200	Weak transcription	Lung	lung
8	chr12:31540800-31573200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:31540800-31576800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:31542000-31578400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:31542200-31583600	Weak transcription	Placenta	Placenta
12	chr12:31542400-31571200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:31542400-31645000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:31542600-31605800	Weak transcription	Colon Smooth Muscle	Colon
15	chr12:31542800-31575400	Weak transcription	Fetal Brain Male	brain
16	chr12:31542800-31578800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:31544200-31579000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:31544400-31581400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:31544600-31584200	Weak transcription	Fetal Lung	lung
20	chr12:31544800-31576200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:31545800-31583600	Weak transcription	Psoas Muscle	Psoas
22	chr12:31548800-31566200	Weak transcription	Fetal Kidney	kidney
23	chr12:31549800-31618000	Weak transcription	Pancreas	Pancrea
24	chr12:31550800-31573200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:31555200-31566200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr12:31555600-31571200	Weak transcription	Aorta	Aorta
27	chr12:31555600-31579600	Weak transcription	HepG2	liver
28	chr12:31556200-31566200	Weak transcription	HSMM	muscle
29	chr12:31556200-31574000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:31556200-31584800	Weak transcription	NHDF-Ad	bronchial
31	chr12:31556200-31587200	Weak transcription	NH-A	brain
32	chr12:31557000-31573000	Weak transcription	Gastric	stomach
33	chr12:31557200-31623600	Weak transcription	Hela-S3	cervix
34	chr12:31558200-31580000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:31560400-31577600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:31560800-31566400	Weak transcription	Osteobl	bone
37	chr12:31561200-31572600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr12:31562200-31571000	Weak transcription	Right Ventricle	heart
39	chr12:31562400-31620600	Weak transcription	Brain Angular Gyrus	brain
40	chr12:31562400-31644400	Weak transcription	Brain Substantia Nigra	brain
41	chr12:31563200-31566400	Weak transcription	Primary B cells from cord blood	blood
42	chr12:31564400-31566600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:31564600-31566600	Strong transcription	Brain Cingulate Gyrus	brain
44	chr12:31564600-31566600	Strong transcription	HSMMtube	muscle
45	chr12:31564600-31567600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:31564600-31568000	Strong transcription	Brain Germinal Matrix	brain
47	chr12:31564600-31568400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:31564600-31569200	Strong transcription	Liver	Liver
49	chr12:31564600-31570000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:31564600-31571000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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