Variant report

Variant	rs182872
Chromosome Location	chr1:220936420-220936421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:220935174..220937582-chr1:220941200..220942748,2	MCF-7	breast:
2	chr1:220934709..220937356-chr1:220938309..220941059,2	K562	blood:
3	chr1:220933592..220936563-chr1:220940646..220943203,2	MCF-7	breast:
4	chr1:220921708..220923550-chr1:220934385..220936474,2	MCF-7	breast:
5	chr1:220935678..220937242-chr1:220938232..220939996,2	MCF-7	breast:
6	chr1:220926792..220928893-chr1:220934076..220936520,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs11118602	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs11118603	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs11118604	0.89[CHB][hapmap]
rs1113125	1.00[EUR][1000 genomes]
rs11557506	1.00[EUR][1000 genomes]
rs12021979	0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12023067	0.82[JPT][hapmap]
rs12023202	1.00[EUR][1000 genomes]
rs12023249	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12023303	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12023484	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12024252	1.00[EUR][1000 genomes]
rs12026135	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12026176	1.00[EUR][1000 genomes]
rs12026612	1.00[EUR][1000 genomes]
rs12026813	0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12027068	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12027298	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12027302	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12027337	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12028887	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12029901	0.82[JPT][hapmap]
rs12030190	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12030249	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12030434	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12030456	1.00[EUR][1000 genomes]
rs12031217	0.82[JPT][hapmap]
rs12031479	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12031951	1.00[EUR][1000 genomes]
rs12032061	0.89[CHB][hapmap]
rs12032336	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12033644	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12033645	1.00[EUR][1000 genomes]
rs12033732	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12033808	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12034685	1.00[EUR][1000 genomes]
rs12034691	1.00[EUR][1000 genomes]
rs12034995	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12035639	0.89[CHB][hapmap]
rs12039043	0.82[JPT][hapmap]
rs12039064	0.82[JPT][hapmap]
rs12039091	0.82[JPT][hapmap]
rs12039436	1.00[EUR][1000 genomes]
rs12041919	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041923	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041952	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041956	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12042585	1.00[JPT][hapmap]
rs12043169	0.89[ASN][1000 genomes]
rs12043238	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12044903	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12045050	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12046425	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12046511	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12046515	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12047809	1.00[EUR][1000 genomes]
rs12047899	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12048193	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048740	1.00[EUR][1000 genomes]
rs12048861	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12049111	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1389745	1.00[EUR][1000 genomes]
rs1389746	1.00[EUR][1000 genomes]
rs1389747	1.00[EUR][1000 genomes]
rs17008639	1.00[EUR][1000 genomes]
rs17008644	1.00[EUR][1000 genomes]
rs17008646	1.00[EUR][1000 genomes]
rs17008649	0.83[EUR][1000 genomes]
rs17008667	1.00[EUR][1000 genomes]
rs17008670	1.00[EUR][1000 genomes]
rs17008680	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs1874115	0.82[JPT][hapmap]
rs1874116	0.82[JPT][hapmap]
rs1874117	0.82[JPT][hapmap]
rs1874123	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs1982894	1.00[EUR][1000 genomes]
rs1982895	1.00[EUR][1000 genomes]
rs2067632	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs2067633	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs2270535	0.82[JPT][hapmap]
rs2275574	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2642446	1.00[JPT][hapmap]
rs337137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337140	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs337144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35297838	1.00[JPT][hapmap]
rs371348	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3767324	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs3795535	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3820349	0.84[ASN][1000 genomes]
rs3820350	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3820352	0.84[ASN][1000 genomes]
rs3820353	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3902885	1.00[EUR][1000 genomes]
rs4124596	1.00[EUR][1000 genomes]
rs419746	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4480363	1.00[EUR][1000 genomes]
rs449699	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs453079	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58538649	0.84[ASN][1000 genomes]
rs60183673	0.82[ASN][1000 genomes]
rs6671579	0.82[JPT][hapmap]
rs6687366	0.82[JPT][hapmap]
rs67065803	1.00[EUR][1000 genomes]
rs67889619	1.00[EUR][1000 genomes]
rs72472377	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72472379	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72472380	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72472383	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72472384	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72472389	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72472390	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72472391	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72472392	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72472394	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72472398	1.00[EUR][1000 genomes]
rs72473905	1.00[EUR][1000 genomes]
rs72473913	1.00[EUR][1000 genomes]
rs746767	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs953970	0.82[JPT][hapmap]
rs9970393	1.00[JPT][hapmap]
rs9970394	0.82[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	nsv523389	chr1:220926844-220956012	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922600-220943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:220922600-220946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:220923200-220948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:220924600-220936800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:220924600-220944000	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:220924800-220945600	Weak transcription	Osteobl	bone
9	chr1:220925000-220946000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:220925000-220959400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:220925200-220942000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:220925200-220943400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:220925400-220950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:220925800-220938400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:220927800-220938600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:220929400-220940600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:220929600-220943000	Weak transcription	Brain Germinal Matrix	brain
18	chr1:220929800-220940800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:220930000-220940600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:220930000-220942400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:220930000-220943400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:220930000-220946000	Weak transcription	Fetal Brain Female	brain
23	chr1:220930000-220950000	Weak transcription	Fetal Brain Male	brain
24	chr1:220930000-220950200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:220930000-220950400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:220930000-220959600	Weak transcription	Psoas Muscle	Psoas
27	chr1:220930200-220937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:220930200-220940800	Weak transcription	NHLF	lung
29	chr1:220930200-220944000	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:220930200-220950000	Weak transcription	Brain Anterior Caudate	brain
31	chr1:220930400-220950000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:220930400-220959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:220930600-220950000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:220930800-220946000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:220931000-220946200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:220931200-220940400	Weak transcription	Fetal Kidney	kidney
37	chr1:220931200-220942400	Weak transcription	Hela-S3	cervix
38	chr1:220931200-220946600	Weak transcription	HUVEC	blood vessel
39	chr1:220931200-220959000	Weak transcription	Brain Substantia Nigra	brain
40	chr1:220931400-220944400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr1:220932800-220937000	Strong transcription	Aorta	Aorta
42	chr1:220932800-220939400	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:220934400-220938400	Strong transcription	Left Ventricle	heart
44	chr1:220934400-220939000	Genic enhancers	Fetal Intestine Small	intestine
45	chr1:220934600-220936600	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:220934600-220936600	Enhancers	Pancreas	Pancrea
47	chr1:220934600-220937000	Genic enhancers	Fetal Heart	heart
48	chr1:220934600-220937000	Strong transcription	Lung	lung
49	chr1:220934600-220937800	Strong transcription	Fetal Lung	lung
50	chr1:220934600-220937800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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