Variant report

Variant	rs1542859
Chromosome Location	chr12:121336766-121336767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121336528..121338127-chr12:121339319..121342244,3	K562	blood:
2	chr12:121326076..121329274-chr12:121333779..121337730,3	MCF-7	breast:
3	chr12:121331922..121335800-chr12:121336708..121340188,4	K562	blood:
4	chr12:121336041..121337901-chr12:121343531..121346196,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10774572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10849791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs10849807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065284	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065293	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065307	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11065332	0.84[ASN][1000 genomes]
rs1151849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1151859	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1151862	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11608262	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11611087	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168944	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168946	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168948	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168953	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1177585	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179939	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12371178	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12372231	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12580949	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]
rs12809299	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12822123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12824150	0.85[CEU][hapmap]
rs12825746	0.83[ASN][1000 genomes]
rs12831094	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1696357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1696390	0.86[ASN][1000 genomes]
rs1718188	0.88[ASN][1000 genomes]
rs2047568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
rs2062507	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs2393716	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2393717	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2650017	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2701177	0.88[ASN][1000 genomes]
rs2701184	0.90[ASN][1000 genomes]
rs2893876	0.81[EUR][1000 genomes]
rs3213566	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs3213570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs3213572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap]
rs34009825	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34076777	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35600816	0.81[ASN][1000 genomes]
rs35706672	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35905305	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809313	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3842985	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3861797	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3883901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3897746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3901854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap]
rs4454799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs471688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4766979	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4766980	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4767935	0.85[CEU][hapmap];0.81[MKK][hapmap]
rs4767937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4767941	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs487943	0.92[ASN][1000 genomes]
rs508595	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs520753	0.91[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs533264	0.92[ASN][1000 genomes]
rs548452	0.93[ASN][1000 genomes]
rs572016	0.83[ASN][1000 genomes]
rs577961	0.83[ASN][1000 genomes]
rs58291418	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58918988	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs590625	0.83[ASN][1000 genomes]
rs602984	0.91[ASN][1000 genomes]
rs609700	0.92[ASN][1000 genomes]
rs610694	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs61946382	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61946383	0.87[ASN][1000 genomes]
rs61946384	0.88[ASN][1000 genomes]
rs61946385	0.87[ASN][1000 genomes]
rs61946386	0.87[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs647881	0.92[ASN][1000 genomes]
rs661647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs665585	0.93[ASN][1000 genomes]
rs666976	0.91[ASN][1000 genomes]
rs7137504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap]
rs73413868	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73415720	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73415734	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7967190	0.83[ASN][1000 genomes]
rs7969140	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7980311	0.90[ASN][1000 genomes]
rs869781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs904628	0.82[ASN][1000 genomes]
rs909053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs989986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs989987	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv975642	chr12:121330910-121340230	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1542859	HPD	cis	parietal	SCAN
rs1542859	SPPL3	cis	cerebellum	SCAN
rs1542859	ACADS	cis	Thyroid	GTEx
rs1542859	SRRM4	cis	cerebellum	SCAN
rs1542859	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs1542859	WSB2	cis	cerebellum	SCAN
rs1542859	SPPL3	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
2	chr12:121294200-121340400	Weak transcription	HSMM	muscle
3	chr12:121297400-121339800	Weak transcription	A549	lung
4	chr12:121304600-121339800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:121312600-121339800	Weak transcription	Brain Germinal Matrix	brain
6	chr12:121312600-121339800	Weak transcription	NHDF-Ad	bronchial
7	chr12:121313400-121339800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:121313400-121339800	Weak transcription	Pancreas	Pancrea
9	chr12:121317400-121338000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:121317600-121339600	Weak transcription	HMEC	breast
11	chr12:121317800-121339600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr12:121318200-121339600	Weak transcription	NHEK	skin
13	chr12:121318200-121340400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:121323200-121340000	Weak transcription	Fetal Lung	lung
15	chr12:121323600-121340600	Weak transcription	Aorta	Aorta
16	chr12:121324000-121340400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:121324400-121339600	Weak transcription	Brain Substantia Nigra	brain
18	chr12:121324400-121339800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:121324600-121339400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:121325800-121338000	Weak transcription	Fetal Brain Female	brain
21	chr12:121325800-121339800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:121326000-121339800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:121326600-121340200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:121328200-121339800	Weak transcription	NHLF	lung
25	chr12:121329000-121339800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:121329000-121340000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:121329000-121340200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:121329000-121340400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:121329200-121339600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:121329200-121339800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:121329200-121339800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:121329200-121340000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr12:121330000-121339600	Weak transcription	Brain Anterior Caudate	brain
34	chr12:121330000-121339800	Weak transcription	Liver	Liver
35	chr12:121330200-121338200	Weak transcription	Esophagus	oesophagus
36	chr12:121330200-121339200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:121330200-121340200	Weak transcription	HUVEC	blood vessel
38	chr12:121330400-121337000	Weak transcription	Brain Angular Gyrus	brain
39	chr12:121330400-121338200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:121330400-121339600	Weak transcription	Adipose Nuclei	Adipose
41	chr12:121330400-121339800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:121330400-121339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:121330400-121339800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:121330400-121339800	Weak transcription	Psoas Muscle	Psoas
45	chr12:121330600-121337800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:121330600-121338800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:121330600-121339000	Weak transcription	Primary B cells from cord blood	blood
48	chr12:121330600-121339600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:121330800-121337000	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr12:121331400-121338000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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