Variant report

Variant	rs12580949
Chromosome Location	chr12:121298164-121298165
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121297144..121299440-chr12:121341037..121343172,2	MCF-7	breast:
2	chr12:121293123..121296169-chr12:121296958..121300717,3	MCF-7	breast:
3	chr12:121297853..121300744-chr12:121301370..121304769,3	K562	blood:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10774572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849791	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs10849807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065284	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065292	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065293	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065301	0.85[CEU][hapmap]
rs11065307	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065332	0.81[ASN][1000 genomes]
rs1151849	1.00[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1151859	0.91[ASN][1000 genomes]
rs1151862	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11608262	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11611087	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168944	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168946	0.92[ASN][1000 genomes]
rs1168948	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168953	0.92[ASN][1000 genomes]
rs1177585	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1179939	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12371178	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12372231	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12579868	0.81[AMR][1000 genomes]
rs12809299	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12822123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12824150	0.84[CEU][hapmap]
rs12825746	0.84[ASN][1000 genomes]
rs12831094	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13746	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs1467283	0.81[AMR][1000 genomes]
rs1542859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1696357	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1696390	0.83[ASN][1000 genomes]
rs1718188	0.84[ASN][1000 genomes]
rs2047568	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs2062507	0.87[CEU][hapmap]
rs2393716	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2393717	0.96[CHB][hapmap];0.90[JPT][hapmap]
rs2461475	0.80[ASN][1000 genomes]
rs2650017	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701177	0.84[ASN][1000 genomes]
rs2701184	0.86[ASN][1000 genomes]
rs2893876	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3213566	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs3213570	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs3213572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs34009825	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34076777	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35600816	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35706672	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35905305	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809313	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3842985	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3861797	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3883901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3897746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3901854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs4454799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471688	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4766979	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4766980	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767935	0.87[CEU][hapmap]
rs4767937	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes]
rs4767941	0.85[ASN][1000 genomes]
rs487943	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs508595	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs520753	0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs533264	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs548452	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs572016	0.84[ASN][1000 genomes]
rs577961	0.84[ASN][1000 genomes]
rs58291418	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58918988	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs590625	0.84[ASN][1000 genomes]
rs602984	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs609700	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610694	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61946382	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61946383	0.83[ASN][1000 genomes]
rs61946384	0.84[ASN][1000 genomes]
rs61946385	0.83[ASN][1000 genomes]
rs61946386	0.83[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs647881	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs661647	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs665585	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs666976	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137504	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs73413868	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73415720	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73415734	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7969140	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980311	0.86[ASN][1000 genomes]
rs869781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs909053	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes]
rs9431	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs989986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs989987	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription 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	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12580949	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs12580949	ACADS	cis	Thyroid	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121282000-121308600	Weak transcription	Fetal Kidney	kidney
2	chr12:121283200-121310200	Weak transcription	Placenta	Placenta
3	chr12:121283400-121307400	Weak transcription	Esophagus	oesophagus
4	chr12:121283600-121302200	Weak transcription	Lung	lung
5	chr12:121287800-121300400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr12:121288000-121300200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:121288000-121311800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:121288000-121316600	Weak transcription	NHLF	lung
9	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
10	chr12:121290000-121300200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:121290000-121302600	Weak transcription	Liver	Liver
12	chr12:121291600-121312400	Weak transcription	Gastric	stomach
13	chr12:121292000-121299200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:121292000-121312400	Weak transcription	Aorta	Aorta
15	chr12:121292400-121305600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:121292800-121303000	Weak transcription	Small Intestine	intestine
17	chr12:121293000-121302600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr12:121293000-121308200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:121293200-121300200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr12:121294200-121303000	Weak transcription	Left Ventricle	heart
21	chr12:121294200-121340400	Weak transcription	HSMM	muscle
22	chr12:121294600-121300200	Weak transcription	Psoas Muscle	Psoas
23	chr12:121294600-121310200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:121295000-121302600	Weak transcription	Brain Substantia Nigra	brain
25	chr12:121295000-121303000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:121295000-121303000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:121295000-121303000	Weak transcription	Thymus	Thymus
28	chr12:121295000-121310200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:121295000-121310200	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:121295000-121311000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:121295000-121316200	Weak transcription	HMEC	breast
32	chr12:121295200-121299000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:121295200-121304200	Weak transcription	Primary T cells from cord blood	blood
34	chr12:121295400-121299400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:121295600-121302800	Weak transcription	Brain Angular Gyrus	brain
36	chr12:121295600-121304200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr12:121295600-121305200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:121295800-121300200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:121295800-121302600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr12:121295800-121302600	Weak transcription	Fetal Thymus	thymus
41	chr12:121295800-121307600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:121296200-121311000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:121296400-121299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr12:121296600-121304400	Weak transcription	Primary B cells from cord blood	blood
45	chr12:121296600-121310800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr12:121296800-121300400	Weak transcription	Brain Hippocampus Middle	brain
47	chr12:121296800-121303400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr12:121296800-121303800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:121296800-121309800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:121297000-121298400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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