Variant report

Variant	rs12489607
Chromosome Location	chr3:50689039-50689040
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50682183..50685016-chr3:50688066..50689856,3	K562	blood:
2	chr3:50652070..50655267-chr3:50687224..50691419,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1077215	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1107312	0.85[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap]
rs11712367	0.82[CHD][hapmap]
rs11917538	0.82[CHD][hapmap]
rs12486143	0.85[AMR][1000 genomes]
rs12486717	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487817	0.83[AMR][1000 genomes]
rs12487821	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs12491440	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491812	0.88[AMR][1000 genomes]
rs12492093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492367	0.82[AFR][1000 genomes]
rs12492540	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492982	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494094	0.90[AMR][1000 genomes]
rs12494326	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12494776	0.80[AFR][1000 genomes]
rs12495399	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17050991	0.88[AMR][1000 genomes]
rs17050995	0.85[AMR][1000 genomes]
rs17051000	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs17051043	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051045	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051403	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17051468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs175634	0.83[CHD][hapmap]
rs1872184	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2035484	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2076927	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2170840	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227292	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2227293	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2239750	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2239751	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239752	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2239753	1.00[ASW][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2285090	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3749265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3752449	0.87[ASN][1000 genomes]
rs375544	0.82[CHD][hapmap]
rs3792323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3792328	0.82[CHD][hapmap]
rs3806706	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs4476497	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4485709	0.82[CHD][hapmap]
rs453570	0.81[CHD][hapmap]
rs4688696	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4688705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688707	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4688709	0.87[ASN][1000 genomes]
rs4688710	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4688713	0.85[AMR][1000 genomes]
rs4688716	0.81[AMR][1000 genomes]
rs56170012	0.83[AMR][1000 genomes]
rs56856095	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57910827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58427389	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs58529408	0.91[ASN][1000 genomes]
rs59036236	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60552073	0.90[AMR][1000 genomes]
rs60552386	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs60602904	0.80[ASN][1000 genomes]
rs60877431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61193866	0.88[AMR][1000 genomes]
rs61316441	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61574029	0.87[AMR][1000 genomes]
rs61613532	0.87[AMR][1000 genomes]
rs616689	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6446208	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6446212	0.82[CHD][hapmap]
rs6446213	0.82[CHD][hapmap]
rs6446222	0.81[CHD][hapmap]
rs650655	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6766638	0.83[AMR][1000 genomes]
rs6771348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779819	0.82[CHD][hapmap]
rs6783922	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794155	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796769	0.82[CHD][hapmap]
rs728902	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72938758	0.87[AMR][1000 genomes]
rs72940708	0.83[EUR][1000 genomes]
rs72942530	0.82[AFR][1000 genomes]
rs72942785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942794	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72944726	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72944730	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73835531	0.85[AMR][1000 genomes]
rs743753	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs745356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7615703	0.82[CHD][hapmap]
rs762889	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs7638082	0.82[CHD][hapmap]
rs808148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs813243	0.82[CHD][hapmap]
rs876103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs876104	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs876105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9814874	0.85[CHB][hapmap]
rs9825535	0.82[CHD][hapmap]
rs9868889	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9869945	0.82[CHD][hapmap]
rs9875961	0.81[CHD][hapmap]
rs9879397	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12489607	MAPKAPK3	cis	lymphoblastoid	seeQTL
rs12489607	HEMK	cis	multi-tissue	Pritchard
rs12489607	HEMK1	cis	lymphoblastoid	seeQTL
rs12489607	HEMK1	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50663400-50690000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:50670400-50699800	Weak transcription	Hela-S3	cervix
3	chr3:50676000-50689200	Strong transcription	Fetal Intestine Small	intestine
4	chr3:50677400-50692200	Weak transcription	NHDF-Ad	bronchial
5	chr3:50680200-50689200	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:50681000-50689200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:50685000-50690000	Enhancers	Fetal Brain Female	brain
8	chr3:50685200-50689200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:50685200-50691600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:50685200-50692800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:50685400-50689200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:50685400-50689800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:50685400-50690200	Enhancers	Fetal Brain Male	brain
14	chr3:50685400-50693000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:50685400-50693000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:50685800-50692400	Weak transcription	Osteobl	bone
17	chr3:50685800-50703800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:50686000-50690400	Enhancers	Left Ventricle	heart
19	chr3:50686000-50690400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:50686400-50692600	Weak transcription	Fetal Thymus	thymus
21	chr3:50686600-50690600	Weak transcription	Adipose Nuclei	Adipose
22	chr3:50686600-50692800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:50686800-50690800	Enhancers	Fetal Heart	heart
24	chr3:50686800-50691800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:50686800-50692000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:50686800-50692400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:50687000-50689200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr3:50687000-50691800	Weak transcription	Pancreas	Pancrea
29	chr3:50687000-50696400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:50687000-50712000	Weak transcription	Right Atrium	heart
31	chr3:50687200-50689400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:50687200-50689400	Weak transcription	Brain Germinal Matrix	brain
33	chr3:50687200-50690200	Weak transcription	Dnd41	blood
34	chr3:50687200-50693000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:50687400-50689200	Enhancers	Right Ventricle	heart
36	chr3:50687400-50689600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:50687400-50689600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr3:50687400-50689800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:50687400-50690400	Enhancers	H1 Cell Line	embryonic stem cell
40	chr3:50687400-50690400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr3:50687400-50692000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr3:50687400-50692200	Weak transcription	HSMM	muscle
43	chr3:50687400-50692600	Weak transcription	Primary B cells from cord blood	blood
44	chr3:50687400-50695600	Weak transcription	HMEC	breast
45	chr3:50687600-50689400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:50687600-50689600	Weak transcription	Fetal Intestine Large	intestine
47	chr3:50687600-50692200	Weak transcription	NHEK	skin
48	chr3:50687600-50692400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:50687600-50692400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:50687600-50694200	Weak transcription	Lung	lung

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