Variant report

Variant	rs62272180
Chromosome Location	chr3:160032281-160032282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160031130..160033296-chr3:160034351..160037164,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10513550	0.98[EUR][1000 genomes]
rs11920289	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12233589	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275150	0.85[AFR][1000 genomes]
rs2275153	0.95[EUR][1000 genomes]
rs2305401	0.86[EUR][1000 genomes]
rs2305406	0.95[EUR][1000 genomes]
rs33999879	0.95[EUR][1000 genomes]
rs3736627	0.82[EUR][1000 genomes]
rs3773371	0.91[EUR][1000 genomes]
rs41272959	0.91[EUR][1000 genomes]
rs55815116	0.95[EUR][1000 genomes]
rs56119270	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56124988	0.86[EUR][1000 genomes]
rs56150006	0.98[EUR][1000 genomes]
rs56401539	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56804721	0.83[AFR][1000 genomes]
rs57030267	0.98[EUR][1000 genomes]
rs57050097	0.89[EUR][1000 genomes]
rs57277659	0.89[EUR][1000 genomes]
rs57285344	0.98[EUR][1000 genomes]
rs57555307	0.89[EUR][1000 genomes]
rs57843971	0.88[ASN][1000 genomes]
rs58627305	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58654032	0.98[EUR][1000 genomes]
rs58776572	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58915028	0.98[EUR][1000 genomes]
rs59695030	0.82[EUR][1000 genomes]
rs59799252	0.91[EUR][1000 genomes]
rs60066272	0.86[EUR][1000 genomes]
rs60153357	0.98[EUR][1000 genomes]
rs60607858	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60914777	0.98[EUR][1000 genomes]
rs61066536	0.98[EUR][1000 genomes]
rs62272176	0.95[EUR][1000 genomes]
rs62272179	0.98[EUR][1000 genomes]
rs62272181	0.98[EUR][1000 genomes]
rs62272185	0.98[EUR][1000 genomes]
rs62272187	0.98[EUR][1000 genomes]
rs62272188	0.98[EUR][1000 genomes]
rs62272190	0.98[EUR][1000 genomes]
rs62272191	0.98[EUR][1000 genomes]
rs62272193	0.98[EUR][1000 genomes]
rs62272196	0.98[EUR][1000 genomes]
rs62272197	0.98[EUR][1000 genomes]
rs62272198	0.98[EUR][1000 genomes]
rs62272205	0.82[EUR][1000 genomes]
rs62272207	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62272231	0.98[EUR][1000 genomes]
rs62272236	0.95[EUR][1000 genomes]
rs62272237	0.95[EUR][1000 genomes]
rs62272245	0.91[EUR][1000 genomes]
rs62272247	0.91[EUR][1000 genomes]
rs62272249	0.89[EUR][1000 genomes]
rs62272251	0.86[EUR][1000 genomes]
rs62272254	0.89[EUR][1000 genomes]
rs62272255	0.89[EUR][1000 genomes]
rs62272256	0.89[EUR][1000 genomes]
rs62272257	0.89[EUR][1000 genomes]
rs62272258	0.89[EUR][1000 genomes]
rs62272259	0.89[EUR][1000 genomes]
rs62272780	0.86[EUR][1000 genomes]
rs62272781	0.86[EUR][1000 genomes]
rs62272783	0.86[EUR][1000 genomes]
rs62272785	0.86[EUR][1000 genomes]
rs62272787	0.86[EUR][1000 genomes]
rs62272788	0.86[EUR][1000 genomes]
rs62272790	0.82[EUR][1000 genomes]
rs62272793	0.82[EUR][1000 genomes]
rs62272799	0.81[EUR][1000 genomes]
rs66769612	0.98[EUR][1000 genomes]
rs66850724	0.91[EUR][1000 genomes]
rs68069205	0.91[EUR][1000 genomes]
rs6808628	0.84[AFR][1000 genomes]
rs73154587	0.93[EUR][1000 genomes]
rs73155914	0.89[EUR][1000 genomes]
rs7614701	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7618017	0.98[EUR][1000 genomes]
rs7645798	0.88[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7648832	0.89[EUR][1000 genomes]
rs9637414	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv979789	chr3:160031241-160032292	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs62272180	IL12A	cis	brain	BrainEAC
rs62272180	B3GALNT1	cis	brain	BrainEAC
rs62272180	PPM1L	cis	brain	BrainEAC
rs62272180	B3GALNT1	cis	cerebellar cortex	BrainEAC

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159971400-160035800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
3	chr3:159975000-160034200	Weak transcription	Fetal Intestine Large	intestine
4	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
9	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:159992400-160035400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:159992800-160033400	Weak transcription	Fetal Kidney	kidney
12	chr3:159992800-160036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:159992800-160036600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:159995400-160034200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:159996400-160037000	Weak transcription	Primary B cells from cord blood	blood
16	chr3:159996600-160038400	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:159996800-160033600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:159997000-160033800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:159997200-160037200	Weak transcription	Brain Angular Gyrus	brain
20	chr3:159997200-160046600	Weak transcription	Fetal Lung	lung
21	chr3:159997600-160035600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr3:159999800-160033800	Weak transcription	Aorta	Aorta
23	chr3:159999800-160034000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:159999800-160035400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:159999800-160047800	Weak transcription	Lung	lung
26	chr3:160010000-160033000	Weak transcription	Fetal Intestine Small	intestine
27	chr3:160010000-160034000	Weak transcription	Pancreas	Pancrea
28	chr3:160010000-160047800	Weak transcription	HepG2	liver
29	chr3:160010000-160048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:160010000-160048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:160010200-160034000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:160012200-160033000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:160014600-160039400	Weak transcription	GM12878-XiMat	blood
34	chr3:160014800-160037200	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:160014800-160039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:160015000-160038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:160015000-160044000	Weak transcription	Osteobl	bone
38	chr3:160015400-160048400	Weak transcription	A549	lung
39	chr3:160015800-160048800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:160018000-160048600	Weak transcription	HSMM	muscle
41	chr3:160020600-160037600	Weak transcription	NH-A	brain
42	chr3:160021000-160033000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:160021200-160043400	Weak transcription	NHDF-Ad	bronchial
44	chr3:160022400-160038800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:160023000-160036800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:160023200-160037800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:160024200-160035600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr3:160024400-160043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:160025400-160033200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:160025400-160033800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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