Variant report

Variant	rs11120082
Chromosome Location	chr1:213229337-213229338
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213227020..213230163-chr1:213238856..213241134,3	K562	blood:
2	chr1:213208745..213211357-chr1:213227758..213229536,2	K562	blood:
3	chr1:213187470..213190491-chr1:213226367..213230214,4	K562	blood:
4	chr1:213228815..213232157-chr1:213233808..213236908,3	K562	blood:
5	chr1:213223540..213226354-chr1:213228669..213231499,2	MCF-7	breast:
6	chr1:213188812..213190491-chr1:213227664..213229877,2	K562	blood:

Variant related genes	Relation type
ENSG00000136643	Chromatin interaction
ENSG00000174606	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10157273	0.85[YRI][hapmap]
rs1045868	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10465694	0.84[EUR][1000 genomes]
rs10735511	0.90[JPT][hapmap]
rs10746440	0.90[JPT][hapmap]
rs10779598	0.90[JPT][hapmap]
rs10864032	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10864033	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10864034	0.82[EUR][1000 genomes]
rs10864036	0.81[EUR][1000 genomes]
rs11120070	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs11120076	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11120080	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11120084	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11120102	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11586518	0.90[JPT][hapmap]
rs12026770	0.85[ASN][1000 genomes]
rs1566247	0.82[EUR][1000 genomes]
rs1566248	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1976333	0.84[EUR][1000 genomes]
rs1995151	0.80[CEU][hapmap]
rs2494767	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs3002284	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs3104207	0.87[ASN][1000 genomes]
rs3738806	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4951476	0.84[EUR][1000 genomes]
rs4951477	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951478	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951479	0.82[EUR][1000 genomes]
rs4951660	0.83[ASN][1000 genomes]
rs4951662	0.80[CEU][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs6540771	0.85[YRI][hapmap]
rs6540774	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6540775	1.00[YRI][hapmap]
rs6540776	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540777	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6540778	0.82[EUR][1000 genomes]
rs6540780	0.81[EUR][1000 genomes]
rs6657234	0.80[CEU][hapmap]
rs6666814	0.82[EUR][1000 genomes]
rs6671019	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6671872	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs6679510	0.85[ASN][1000 genomes]
rs6691488	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6692011	0.85[YRI][hapmap]
rs6692144	0.80[CEU][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs6697921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6699158	0.81[EUR][1000 genomes]
rs7516436	0.85[YRI][hapmap]
rs7517229	0.83[EUR][1000 genomes]
rs7520067	0.85[YRI][hapmap]
rs7537285	0.86[ASN][1000 genomes]
rs7540350	0.89[ASN][1000 genomes]
rs7547782	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9645358	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11120082	BATF3	cis	parietal	SCAN
rs11120082	ANGEL2	cis	parietal	SCAN
rs11120082	RPS6KC1	cis	Artery Tibial	GTEx
rs11120082	TNNI1	trans	parietal	SCAN
rs11120082	ANGEL2	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213225200-213253400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:213225200-213254400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:213225400-213229600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:213225400-213229600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:213225400-213254000	Weak transcription	Aorta	Aorta
6	chr1:213225400-213254000	Weak transcription	Left Ventricle	heart
7	chr1:213225400-213256600	Weak transcription	Ovary	ovary
8	chr1:213225600-213229400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:213225600-213229800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:213225600-213229800	Weak transcription	Fetal Intestine Small	intestine
11	chr1:213225600-213234000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:213225600-213236000	Weak transcription	Right Atrium	heart
13	chr1:213225600-213243600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:213225600-213244000	Weak transcription	HSMM	muscle
15	chr1:213225800-213229600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr1:213225800-213229800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:213225800-213230200	Weak transcription	Fetal Intestine Large	intestine
18	chr1:213225800-213230200	Weak transcription	Psoas Muscle	Psoas
19	chr1:213225800-213234200	Weak transcription	Primary B cells from cord blood	blood
20	chr1:213225800-213252800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:213225800-213254000	Weak transcription	Primary T cells from cord blood	blood
22	chr1:213226000-213233200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:213226000-213254000	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:213226200-213243800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:213226200-213252800	Weak transcription	Fetal Stomach	stomach
26	chr1:213226400-213229400	Weak transcription	NHDF-Ad	bronchial
27	chr1:213226400-213229800	Weak transcription	Brain Substantia Nigra	brain
28	chr1:213226400-213230200	Weak transcription	Pancreas	Pancrea
29	chr1:213226600-213231400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:213226600-213232000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:213226800-213229400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:213226800-213230600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:213226800-213237400	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:213227000-213229400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:213227000-213229800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:213227000-213230800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr1:213227000-213232000	Weak transcription	GM12878-XiMat	blood
38	chr1:213227000-213254000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:213227200-213243000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:213227800-213230600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:213227800-213231800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:213228000-213254200	Weak transcription	Brain Hippocampus Middle	brain
43	chr1:213228200-213229400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:213228400-213229400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:213228600-213229400	Enhancers	Hela-S3	cervix
46	chr1:213228600-213232000	Enhancers	HepG2	liver
47	chr1:213228600-213244000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:213228800-213229400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr1:213228800-213229400	Enhancers	Muscle Satellite Cultured Cells	--
50	chr1:213228800-213238800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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