Variant report

Variant	rs12462557
Chromosome Location	chr19:44774830-44774831
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	chr19:44717507..44719170-chr19:44774754..44776983,2	K562	blood:
2	chr19:44762511..44764664-chr19:44772630..44774873,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159915	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10405450	0.81[EUR][1000 genomes]
rs10410086	0.81[EUR][1000 genomes]
rs10423306	0.82[EUR][1000 genomes]
rs10425945	0.85[CEU][hapmap]
rs10775542	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666199	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11667521	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11671074	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12459795	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12460431	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12461251	0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12462723	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12609635	0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]
rs12972784	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12975315	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12975546	1.00[CEU][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12980565	1.00[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2014501	0.87[EUR][1000 genomes]
rs2051058	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2051059	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2085516	0.85[GIH][hapmap]
rs2100643	0.82[GIH][hapmap]
rs2125578	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2125579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2168989	0.85[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap]
rs2232801	0.85[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2279072	0.89[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2279073	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2293587	0.85[GIH][hapmap]
rs2356727	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2356751	0.83[GIH][hapmap]
rs3817595	0.85[GIH][hapmap]
rs4592768	0.86[AMR][1000 genomes]
rs4802210	0.85[GIH][hapmap];0.91[JPT][hapmap]
rs4802217	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4802218	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4803694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509145	0.91[JPT][hapmap]
rs6509146	0.85[GIH][hapmap]
rs6509150	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249209	0.83[GIH][hapmap]
rs7251134	0.83[MEX][hapmap]
rs7251682	0.89[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs7252577	0.87[EUR][1000 genomes]
rs7253196	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7253533	0.84[CEU][hapmap]
rs7259916	0.81[EUR][1000 genomes]
rs7260304	0.88[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap]
rs7508523	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8101032	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8102037	0.82[EUR][1000 genomes]
rs8103838	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs8105073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8105479	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AFR][1000 genomes]
rs8106766	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8108934	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8109462	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8109706	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9304640	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9646642	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9646643	0.93[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12462557	RUVBL2	cis	parietal	SCAN
rs12462557	ZNF528	cis	parietal	SCAN
rs12462557	AKT1S1	cis	cerebellum	SCAN
rs12462557	ZNF233	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44730000-44775600	ZNF genes & repeats	Liver	Liver
2	chr19:44764600-44778200	Weak transcription	HSMMtube	muscle
3	chr19:44764800-44777600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:44764800-44777600	Weak transcription	Placenta	Placenta
5	chr19:44764800-44782000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:44765000-44775400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr19:44765000-44777400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr19:44765000-44777400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:44765000-44777400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:44765000-44777400	Weak transcription	Fetal Heart	heart
11	chr19:44765000-44777600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr19:44765000-44777600	Weak transcription	Right Ventricle	heart
13	chr19:44765000-44778000	Weak transcription	Fetal Brain Male	brain
14	chr19:44765200-44777000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr19:44765200-44777600	Weak transcription	Dnd41	blood
16	chr19:44765400-44777600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr19:44767600-44777400	Weak transcription	Brain Angular Gyrus	brain
18	chr19:44769800-44775200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
19	chr19:44769800-44775600	Strong transcription	Primary T cells from cord blood	blood
20	chr19:44770000-44780800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:44770600-44777400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:44770600-44777600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:44771000-44775600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:44771000-44777600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:44771200-44775200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:44771400-44777600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:44771400-44777600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:44771400-44778200	Weak transcription	Fetal Kidney	kidney
29	chr19:44771600-44777400	Weak transcription	Primary B cells from cord blood	blood
30	chr19:44771600-44777600	Weak transcription	Thymus	Thymus
31	chr19:44772200-44777200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr19:44772200-44777200	Weak transcription	Fetal Muscle Leg	muscle
33	chr19:44772200-44777400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr19:44772200-44777400	Weak transcription	Psoas Muscle	Psoas
35	chr19:44772200-44777600	Weak transcription	Left Ventricle	heart
36	chr19:44772800-44777200	Weak transcription	Brain Hippocampus Middle	brain
37	chr19:44772800-44777400	Weak transcription	Brain Substantia Nigra	brain
38	chr19:44772800-44777400	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:44772800-44777600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:44773000-44777400	Weak transcription	Brain Anterior Caudate	brain
41	chr19:44773000-44777400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr19:44773000-44778000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr19:44773200-44777400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:44774000-44775000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
45	chr19:44774000-44776000	Strong transcription	Brain Germinal Matrix	brain
46	chr19:44774400-44775000	ZNF genes & repeats	Pancreas	Pancrea
47	chr19:44774400-44776200	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr19:44774600-44775000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:44774600-44775000	ZNF genes & repeats	Aorta	Aorta
50	chr19:44774600-44775000	ZNF genes & repeats	Fetal Stomach	stomach

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