Variant report

Variant	rs1864892
Chromosome Location	chr12:105709809-105709810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11112432	0.81[TSI][hapmap]
rs11112446	0.86[AFR][1000 genomes]
rs11112450	0.88[AFR][1000 genomes]
rs11831950	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11836865	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12578730	0.86[AFR][1000 genomes]
rs1469663	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1469665	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4964131	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964132	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4964359	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56032632	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56130330	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66467637	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67114583	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67454169	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73181867	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73181871	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1864892	TDG	cis	parietal	SCAN
rs1864892	APPL2	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105704200-105711000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr12:105706400-105715000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr12:105706600-105711000	Weak transcription	Fetal Kidney	kidney
4	chr12:105708400-105710200	Enhancers	Stomach Mucosa	stomach
5	chr12:105708600-105710000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr12:105708600-105710000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr12:105708600-105710000	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr12:105708600-105710000	Enhancers	Esophagus	oesophagus
9	chr12:105708600-105711600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:105708600-105711600	Enhancers	HMEC	breast
11	chr12:105708600-105712400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr12:105708800-105711000	Enhancers	A549	lung
13	chr12:105708800-105712200	Enhancers	NHEK	skin
14	chr12:105709000-105711000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:105709000-105711600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:105709200-105711800	Enhancers	Fetal Intestine Large	intestine
17	chr12:105709200-105711800	Enhancers	NHDF-Ad	bronchial
18	chr12:105709200-105712000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr12:105709200-105712600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr12:105709400-105710000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:105709400-105710000	Enhancers	Gastric	stomach
22	chr12:105709400-105710000	Enhancers	Lung	lung
23	chr12:105709400-105710000	Enhancers	Pancreas	Pancrea
24	chr12:105709400-105710000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr12:105709400-105711200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:105709400-105711600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr12:105709400-105711600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:105709400-105712200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:105709400-105712400	Enhancers	HSMM	muscle
30	chr12:105709400-105712600	Enhancers	Osteobl	bone
31	chr12:105709400-105717200	Enhancers	Fetal Intestine Small	intestine
32	chr12:105709600-105710200	Enhancers	HSMMtube	muscle
33	chr12:105709600-105710800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:105709600-105711000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:105709600-105711000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:105709600-105711000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:105709600-105711400	Weak transcription	Hela-S3	cervix
38	chr12:105709600-105712600	Enhancers	NHLF	lung
39	chr12:105709600-105713400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:105709800-105710800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr12:105709800-105713800	Weak transcription	Primary T cells from cord blood	blood
42	chr12:105709800-105714600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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