Variant report

Variant	rs10743645
Chromosome Location	chr12:29318018-29318019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10743647	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10743648	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10743649	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10771486	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771489	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771492	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10771494	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10843343	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11050084	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050098	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050099	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050104	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050108	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050110	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050112	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050114	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12310732	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12366549	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1496218	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1561132	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1826800	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1845819	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1908690	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1908691	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2349974	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4105125	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4105126	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4105127	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4105128	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4141943	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4141945	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4323913	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4536271	0.93[ASN][1000 genomes]
rs4930856	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4930857	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930858	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930859	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4931158	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931162	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4931163	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4931165	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60287933	0.98[ASN][1000 genomes]
rs6487778	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487783	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71453727	1.00[ASN][1000 genomes]
rs7294355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296268	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7297542	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73265795	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7968949	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974769	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975191	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7980923	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs924105	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924107	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs924109	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs958478	0.91[EUR][1000 genomes];0.91[ASN][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10743645	RP11-996F15.2	cis	Thyroid	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29306600-29324600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:29306800-29324400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:29308400-29324000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:29308400-29324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:29313400-29319400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:29315800-29320200	Enhancers	Small Intestine	intestine
7	chr12:29316200-29324200	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr12:29316200-29324400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:29316800-29318200	Enhancers	Adipose Nuclei	Adipose
10	chr12:29316800-29318800	Enhancers	Colon Smooth Muscle	Colon
11	chr12:29316800-29323800	Enhancers	Fetal Intestine Large	intestine
12	chr12:29317000-29318200	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr12:29317000-29318400	Enhancers	Colonic Mucosa	Colon
14	chr12:29317000-29318400	Enhancers	K562	blood
15	chr12:29317000-29319000	Enhancers	HUVEC	blood vessel
16	chr12:29317000-29320800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:29317000-29324000	Enhancers	Fetal Intestine Small	intestine
18	chr12:29317200-29318200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr12:29317200-29318200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:29317200-29318200	Enhancers	Dnd41	blood
21	chr12:29317200-29318400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:29317200-29318400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:29317200-29318400	Enhancers	NHLF	lung
24	chr12:29317200-29318600	Enhancers	Primary B cells from peripheral blood	blood
25	chr12:29317200-29318800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:29317200-29318800	Enhancers	Stomach Mucosa	stomach
27	chr12:29317200-29319000	Enhancers	Primary B cells from cord blood	blood
28	chr12:29317400-29318200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:29317400-29318200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:29317400-29318200	Enhancers	NH-A	brain
31	chr12:29317400-29318400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:29317400-29318400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr12:29317400-29318400	Enhancers	NHDF-Ad	bronchial
34	chr12:29317400-29318400	Enhancers	NHEK	skin
35	chr12:29317400-29318600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:29317400-29318800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:29317400-29319000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr12:29317600-29318200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr12:29317600-29318200	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr12:29317600-29318200	Enhancers	HMEC	breast
41	chr12:29317600-29318200	Enhancers	HSMM	muscle
42	chr12:29317600-29318400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr12:29317600-29318400	Enhancers	Fetal Lung	lung
44	chr12:29317600-29318800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:29317600-29322000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:29317600-29324400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:29317600-29324400	Weak transcription	Lung	lung
48	chr12:29317600-29340800	Weak transcription	Left Ventricle	heart
49	chr12:29317800-29318200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:29317800-29318200	Enhancers	Fetal Kidney	kidney

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