Variant report

Variant	rs12043238
Chromosome Location	chr1:220930685-220930686
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:220926710..220928570-chr1:220929149..220931113,2	MCF-7	breast:
2	chr1:220925438..220927343-chr1:220929690..220931741,2	K562	blood:
3	chr1:220920704..220923005-chr1:220929506..220932087,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117791	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10863563	0.81[ASN][1000 genomes]
rs11118602	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11118603	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11118604	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1113125	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11557506	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12021979	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023067	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12023149	0.80[ASN][1000 genomes]
rs12023202	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12023249	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12023303	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12023484	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12024252	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12026135	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12026176	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12026612	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12026813	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12027068	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12027298	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12027302	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12027337	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12028584	0.81[ASN][1000 genomes]
rs12028887	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12029763	0.81[ASN][1000 genomes]
rs12029901	1.00[JPT][hapmap]
rs12030190	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12030249	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12030434	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12030456	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12031217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12031479	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12031951	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12032061	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12032336	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12033121	0.81[ASN][1000 genomes]
rs12033644	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12033645	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12033732	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12033808	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs12034685	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12034691	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12034995	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12035639	0.86[CHB][hapmap]
rs12038224	0.84[CHB][hapmap]
rs12038621	0.88[ASN][1000 genomes]
rs12039043	1.00[JPT][hapmap]
rs12039064	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12039091	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12039436	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12041919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041923	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041952	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042585	1.00[JPT][hapmap]
rs12043169	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12043252	0.81[ASN][1000 genomes]
rs12044903	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12045050	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12045953	0.88[CHB][hapmap]
rs12046425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046511	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047809	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12047899	0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12048193	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12048740	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12048861	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12049111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1389745	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1389746	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1389747	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17008639	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17008644	0.83[EUR][1000 genomes]
rs17008646	0.83[EUR][1000 genomes]
rs17008649	0.81[ASN][1000 genomes]
rs17008667	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17008670	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17008680	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs182872	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1874115	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1874116	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1874117	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1874123	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1982894	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1982895	0.86[CHB][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2067632	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2067633	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2270535	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2275574	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28525291	0.81[ASN][1000 genomes]
rs337137	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337140	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337141	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs337144	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35297838	1.00[JPT][hapmap]
rs371348	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3767324	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3795535	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806326	0.81[ASN][1000 genomes]
rs3806328	0.81[ASN][1000 genomes]
rs3820349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3820350	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820352	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3820353	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820357	0.81[ASN][1000 genomes]
rs3902885	0.83[EUR][1000 genomes]
rs4124596	0.83[EUR][1000 genomes]
rs419746	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4480363	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs449699	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs453079	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58538649	0.95[ASN][1000 genomes]
rs60183673	0.93[ASN][1000 genomes]
rs6671579	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6687366	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs67065803	0.83[EUR][1000 genomes]
rs67889619	0.83[EUR][1000 genomes]
rs72470443	0.81[ASN][1000 genomes]
rs72470444	0.81[ASN][1000 genomes]
rs72470571	0.81[ASN][1000 genomes]
rs72470575	0.81[ASN][1000 genomes]
rs72470581	0.81[ASN][1000 genomes]
rs72470584	0.81[ASN][1000 genomes]
rs72472377	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72472379	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72472380	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72472383	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72472384	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72472389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72472390	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72472391	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72472392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72472394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72472398	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72472399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72472402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72473905	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72473913	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs746767	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs953970	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9970128	0.81[ASN][1000 genomes]
rs9970130	0.81[ASN][1000 genomes]
rs9970393	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9970394	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9970623	0.81[ASN][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	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:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220922400-220932200	Weak transcription	HSMMtube	muscle
2	chr1:220922600-220931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:220922600-220943800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:220922600-220946400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:220922800-220959600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:220922800-220959600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:220923200-220948000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:220924200-220931000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:220924200-220936000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:220924600-220936800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:220924600-220944000	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:220924800-220931200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:220924800-220945600	Weak transcription	Osteobl	bone
14	chr1:220925000-220946000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:220925000-220959400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:220925200-220942000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:220925200-220943400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:220925400-220950200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr1:220925800-220931800	Strong transcription	Fetal Intestine Small	intestine
20	chr1:220925800-220938400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:220927000-220933000	Weak transcription	Right Ventricle	heart
22	chr1:220927200-220933200	Weak transcription	Small Intestine	intestine
23	chr1:220927600-220930800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:220927600-220931200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:220927600-220931200	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:220927600-220931200	Strong transcription	Hela-S3	cervix
27	chr1:220927600-220934400	Weak transcription	Stomach Mucosa	stomach
28	chr1:220927800-220930800	Strong transcription	Gastric	stomach
29	chr1:220927800-220931000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:220927800-220931000	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:220927800-220931200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr1:220927800-220931200	Strong transcription	Fetal Intestine Large	intestine
33	chr1:220927800-220931200	Strong transcription	Pancreas	Pancrea
34	chr1:220927800-220931400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:220927800-220931600	Strong transcription	Lung	lung
36	chr1:220927800-220938600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:220928000-220931000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:220928000-220931200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:220928000-220931200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:220928000-220931200	Strong transcription	Ovary	ovary
41	chr1:220928000-220931200	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:220928000-220933600	Strong transcription	Fetal Stomach	stomach
43	chr1:220928200-220930800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:220928200-220931200	Strong transcription	HUVEC	blood vessel
45	chr1:220928400-220930800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr1:220928400-220931200	Strong transcription	Left Ventricle	heart
47	chr1:220928400-220931200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr1:220928600-220931200	Strong transcription	A549	lung
49	chr1:220928800-220931200	Strong transcription	Brain Substantia Nigra	brain
50	chr1:220929000-220931200	Strong transcription	Adipose Nuclei	Adipose

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