Variant report

Variant	rs1466020
Chromosome Location	chr2:98365250-98365251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:98278220..98280235-chr2:98364964..98367550,2	K562	blood:
2	chr2:98326428..98327307-chr2:98364548..98365267,2	MCF-7	breast:
3	chr2:98314807..98317005-chr2:98364935..98367106,2	K562	blood:
4	chr2:98316327..98317224-chr2:98364607..98365532,3	MCF-7	breast:
5	chr2:98316391..98316923-chr2:98364533..98365419,2	MCF-7	breast:
6	chr2:98364771..98366916-chr2:98367018..98368855,2	MCF-7	breast:
7	chr2:98261461..98264004-chr2:98363822..98366749,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135940	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10176201	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10182941	0.94[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1071885	0.82[AMR][1000 genomes]
rs11123869	1.00[LWK][hapmap];0.94[MKK][hapmap]
rs11123924	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11123949	0.82[AMR][1000 genomes]
rs11899171	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12712123	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12712174	0.94[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs13010946	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1317178	0.94[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13405546	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1466924	0.87[AMR][1000 genomes]
rs1922282	0.94[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]
rs2091772	0.89[AMR][1000 genomes]
rs2100058	0.84[AMR][1000 genomes]
rs2141862	0.82[AMR][1000 genomes]
rs2305142	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2309316	0.94[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2309317	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3762593	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4274643	0.94[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4560167	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5865	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs6543108	0.94[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6543109	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6543161	0.84[AMR][1000 genomes]
rs6543177	0.84[AMR][1000 genomes]
rs6543210	0.94[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]
rs6707924	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6709571	0.94[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs6710813	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6712517	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6719556	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6723653	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6744331	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6748809	0.80[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs6748927	0.83[CHB][hapmap]
rs7558931	0.94[CEU][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7561104	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7562695	0.84[AMR][1000 genomes]
rs7567397	0.94[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7574437	0.86[AMR][1000 genomes]
rs7582664	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs873886	1.00[LWK][hapmap];0.85[YRI][hapmap]
rs930607	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9308862	0.86[AMR][1000 genomes]
rs956696	0.82[AMR][1000 genomes]
rs9973416	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]

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	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1466020	ADRA2B	cis	cerebellum	SCAN
rs1466020	ANKRD36B	cis	Artery Tibial	GTEx
rs1466020	ANKRD36B	cis	Skin Sun Exposed Lower leg	GTEx
rs1466020	FAM178B	cis	parietal	SCAN
rs1466020	ANKRD36B	cis	Nerve Tibial	GTEx
rs1466020	CNNM3	cis	cerebellum	SCAN
rs1466020	TMEM131	Cis_1M	lymphoblastoid	RTeQTL
rs1466020	ANKRD36B	cis	lung	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98345000-98366400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr2:98348200-98372400	Weak transcription	Esophagus	oesophagus
3	chr2:98352200-98398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:98354400-98368200	Weak transcription	Colonic Mucosa	Colon
5	chr2:98355000-98373200	Weak transcription	Gastric	stomach
6	chr2:98357000-98365400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:98357200-98367400	Weak transcription	Brain Substantia Nigra	brain
8	chr2:98357400-98366000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:98357400-98368000	Weak transcription	Lung	lung
10	chr2:98357400-98368600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:98357400-98371400	Weak transcription	Dnd41	blood
12	chr2:98357400-98372000	Weak transcription	Pancreas	Pancrea
13	chr2:98357600-98365800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr2:98358600-98372000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:98358800-98371600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:98359000-98366600	Weak transcription	Liver	Liver
17	chr2:98359000-98368400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:98359000-98368400	Weak transcription	NHLF	lung
19	chr2:98359200-98368000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:98359200-98368000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:98359200-98368600	Weak transcription	NH-A	brain
22	chr2:98359200-98368600	Weak transcription	Osteobl	bone
23	chr2:98359200-98371000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:98359200-98371200	Weak transcription	Small Intestine	intestine
25	chr2:98359200-98371800	Weak transcription	Right Ventricle	heart
26	chr2:98359200-98382400	Weak transcription	Psoas Muscle	Psoas
27	chr2:98359600-98365400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr2:98359600-98365400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr2:98359600-98367600	Weak transcription	HMEC	breast
30	chr2:98359600-98368000	Weak transcription	Right Atrium	heart
31	chr2:98359600-98371000	Weak transcription	Brain Angular Gyrus	brain
32	chr2:98359600-98371000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:98360200-98371200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr2:98360400-98365400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:98360800-98368400	Weak transcription	NHEK	skin
36	chr2:98360800-98369000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:98361000-98366200	Weak transcription	Fetal Intestine Small	intestine
38	chr2:98361000-98366600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:98361000-98366800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:98361000-98368200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:98361000-98373200	Weak transcription	Ovary	ovary
42	chr2:98361200-98365400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:98361200-98366400	Weak transcription	Fetal Lung	lung
44	chr2:98361200-98366400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:98361200-98366600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:98361200-98366600	Weak transcription	Fetal Intestine Large	intestine
47	chr2:98361200-98369200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:98361200-98370600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:98361200-98371200	Weak transcription	Brain Anterior Caudate	brain
50	chr2:98361200-98371200	Weak transcription	HepG2	liver

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