Variant report

Variant	rs12494326
Chromosome Location	chr3:50629659-50629660
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50619029..50623920-chr3:50628439..50631863,6	MCF-7	breast:
2	chr3:50626963..50632967-chr3:50633102..50640850,17	K562	blood:
3	chr3:50628346..50630118-chr3:50630159..50631667,2	K562	blood:
4	chr3:50373283..50375179-chr3:50628099..50629675,2	K562	blood:
5	chr3:50624179..50629741-chr3:50646689..50652947,9	K562	blood:

Variant related genes	Relation type
ENSG00000068028	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000114737	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1077215	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1107312	0.88[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs12486143	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486717	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12487817	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12489607	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12491440	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12491812	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12492093	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12492540	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12492982	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12494094	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12495399	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs17050991	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17050995	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17051000	0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17051043	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17051045	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17051403	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1872184	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1894459	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2035484	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2076927	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2170840	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2227292	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2227293	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239750	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2239751	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2239752	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239753	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285090	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3749265	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3752449	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3792323	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3806706	0.89[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4476497	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4640555	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4688696	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4688705	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4688707	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688709	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4688710	0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4688713	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4688715	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4688716	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs56170012	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56856095	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57910827	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58427389	0.91[ASN][1000 genomes]
rs58529408	0.80[ASN][1000 genomes]
rs59036236	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60552073	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60877431	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61193866	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61316441	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61574029	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61613532	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs616689	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6446208	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs650655	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6766638	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6771348	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6783922	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6794155	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs728902	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72938758	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72942785	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72942794	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72944726	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72944730	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs73835531	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs743753	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs745356	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs762889	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs808148	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs876103	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs876104	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs876105	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9814874	0.89[CHB][hapmap]
rs9868889	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9879397	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS 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	27 gene(s)	inside rSNPs	diseases
9	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12494326	HEMK1	cis	multi-tissue	Pritchard
rs12494326	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
2	chr3:50622400-50629800	Weak transcription	Fetal Lung	lung
3	chr3:50623000-50636600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:50623200-50633800	Enhancers	Fetal Thymus	thymus
5	chr3:50625200-50630600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:50626800-50632400	Enhancers	Liver	Liver
7	chr3:50627200-50629800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:50627800-50630000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr3:50628000-50630000	Enhancers	Osteobl	bone
10	chr3:50628000-50630400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:50628000-50630600	Enhancers	Stomach Mucosa	stomach
12	chr3:50628000-50630600	Enhancers	Spleen	Spleen
13	chr3:50628000-50630800	Enhancers	Esophagus	oesophagus
14	chr3:50628000-50630800	Enhancers	Fetal Muscle Trunk	muscle
15	chr3:50628000-50630800	Enhancers	Gastric	stomach
16	chr3:50628000-50630800	Enhancers	Pancreas	Pancrea
17	chr3:50628000-50630800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr3:50628000-50630800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr3:50628000-50631000	Enhancers	Fetal Muscle Leg	muscle
20	chr3:50628000-50631200	Enhancers	Placenta	Placenta
21	chr3:50628000-50631200	Enhancers	Left Ventricle	heart
22	chr3:50628000-50631200	Enhancers	Lung	lung
23	chr3:50628200-50630400	Enhancers	Small Intestine	intestine
24	chr3:50628200-50632400	Enhancers	Fetal Heart	heart
25	chr3:50628400-50630600	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:50628400-50630800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:50628400-50632000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:50628400-50633800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:50628600-50629800	Enhancers	Colon Smooth Muscle	Colon
30	chr3:50628600-50630600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:50628600-50630600	Enhancers	Stomach Smooth Muscle	stomach
32	chr3:50628600-50630600	Enhancers	NHEK	skin
33	chr3:50628600-50630800	Enhancers	Duodenum Mucosa	Duodenum
34	chr3:50628600-50631000	Enhancers	Primary hematopoietic stem cells	blood
35	chr3:50628600-50633600	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr3:50628600-50635600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:50628600-50638200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr3:50628800-50629800	Enhancers	GM12878-XiMat	blood
39	chr3:50628800-50629800	Weak transcription	HMEC	breast
40	chr3:50628800-50629800	Weak transcription	HSMM	muscle
41	chr3:50628800-50630000	Weak transcription	Fetal Intestine Large	intestine
42	chr3:50628800-50630000	Weak transcription	Ovary	ovary
43	chr3:50628800-50630400	Enhancers	Primary B cells from cord blood	blood
44	chr3:50628800-50630600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:50628800-50630800	Enhancers	Adipose Nuclei	Adipose
46	chr3:50628800-50630800	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr3:50628800-50631000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:50628800-50631200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:50628800-50631200	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr3:50628800-50631400	Enhancers	Primary T cells from cord blood	blood

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