Variant report

Variant	rs4688705
Chromosome Location	chr3:50690570-50690571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50653119..50654010-chr3:50690263..50690785,3	MCF-7	breast:
2	chr3:50653143..50653987-chr3:50690312..50690824,2	K562	blood:
3	chr3:50690479..50693094-chr3:50743826..50746673,2	K562	blood:
4	chr3:50652070..50655267-chr3:50687224..50691419,6	MCF-7	breast:
5	chr3:50653442..50654310-chr3:50689845..50690772,2	MCF-7	breast:
6	chr3:50660634..50661225-chr3:50689949..50690821,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1013233	0.88[AFR][1000 genomes]
rs1077215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1107312	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs12486143	0.86[AMR][1000 genomes]
rs12486717	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12487817	0.87[AMR][1000 genomes]
rs12487821	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12489607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491812	0.89[AMR][1000 genomes]
rs12492093	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492540	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492982	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494094	0.81[AMR][1000 genomes]
rs12494326	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12495399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1385025	0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs17050991	0.89[AMR][1000 genomes]
rs17050995	0.86[AMR][1000 genomes]
rs17051000	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs17051043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17051468	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1872184	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1894459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1971976	0.84[AFR][1000 genomes]
rs2035484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2076927	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2170840	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2227293	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2239750	0.87[ASN][1000 genomes]
rs2239751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2239753	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2285090	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34848480	0.86[AFR][1000 genomes]
rs3749265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3752449	0.87[ASN][1000 genomes]
rs375544	0.84[AFR][1000 genomes]
rs3792323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3792325	0.82[AFR][1000 genomes]
rs3792328	0.84[AFR][1000 genomes]
rs3804632	0.83[AFR][1000 genomes]
rs3806706	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs3943212	0.84[AFR][1000 genomes]
rs396302	0.83[AFR][1000 genomes]
rs443436	0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs4476497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs448028	0.83[AFR][1000 genomes]
rs4688696	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4688707	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4688709	0.87[ASN][1000 genomes]
rs4688710	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4688713	0.86[AMR][1000 genomes]
rs56170012	0.84[AMR][1000 genomes]
rs56856095	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57910827	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58427389	0.95[ASN][1000 genomes]
rs58529408	0.91[ASN][1000 genomes]
rs59036236	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60552073	0.81[AMR][1000 genomes]
rs60552386	0.82[ASN][1000 genomes]
rs60602904	0.80[ASN][1000 genomes]
rs60877431	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs609678	0.93[YRI][hapmap]
rs61193866	0.89[AMR][1000 genomes]
rs61316441	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61574029	0.90[AMR][1000 genomes]
rs61613532	0.90[AMR][1000 genomes]
rs616589	0.84[AFR][1000 genomes]
rs616689	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];0.94[ASN][1000 genomes]
rs6446208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6446212	0.84[AFR][1000 genomes]
rs650655	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs667894	0.93[YRI][hapmap]
rs6766638	0.87[AMR][1000 genomes]
rs6771348	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794155	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs728901	0.88[AFR][1000 genomes]
rs728902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72938758	0.90[AMR][1000 genomes]
rs72942785	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942794	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72944726	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72944730	0.91[ASN][1000 genomes]
rs73835531	0.86[AMR][1000 genomes]
rs743753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs745356	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs751851	0.86[AFR][1000 genomes]
rs762889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs808148	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs808149	0.88[AFR][1000 genomes]
rs813243	0.81[AFR][1000 genomes]
rs876103	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs876104	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs876105	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs900735	0.88[AFR][1000 genomes]
rs9682401	0.88[AFR][1000 genomes]
rs9814874	0.86[CHB][hapmap]
rs9868889	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9879397	1.00[CHB][hapmap];1.00[JPT][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]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4688705	HEMK1	cis	multi-tissue	Pritchard
rs4688705	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50670400-50699800	Weak transcription	Hela-S3	cervix
2	chr3:50677400-50692200	Weak transcription	NHDF-Ad	bronchial
3	chr3:50685200-50691600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:50685200-50692800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:50685400-50693000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:50685400-50693000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:50685800-50692400	Weak transcription	Osteobl	bone
8	chr3:50685800-50703800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:50686400-50692600	Weak transcription	Fetal Thymus	thymus
10	chr3:50686600-50690600	Weak transcription	Adipose Nuclei	Adipose
11	chr3:50686600-50692800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:50686800-50690800	Enhancers	Fetal Heart	heart
13	chr3:50686800-50691800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:50686800-50692000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:50686800-50692400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr3:50687000-50691800	Weak transcription	Pancreas	Pancrea
17	chr3:50687000-50696400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:50687000-50712000	Weak transcription	Right Atrium	heart
19	chr3:50687200-50693000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:50687400-50692000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:50687400-50692200	Weak transcription	HSMM	muscle
22	chr3:50687400-50692600	Weak transcription	Primary B cells from cord blood	blood
23	chr3:50687400-50695600	Weak transcription	HMEC	breast
24	chr3:50687600-50692200	Weak transcription	NHEK	skin
25	chr3:50687600-50692400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr3:50687600-50692400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:50687600-50694200	Weak transcription	Lung	lung
28	chr3:50687600-50697400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:50687600-50702400	Weak transcription	Spleen	Spleen
30	chr3:50688000-50691800	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr3:50688000-50692000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr3:50688000-50692200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:50688000-50692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:50688000-50692200	Weak transcription	Esophagus	oesophagus
35	chr3:50688000-50692800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:50688000-50693600	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:50688200-50691400	Weak transcription	Primary T cells from cord blood	blood
38	chr3:50688200-50702600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:50688600-50690600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:50688800-50691600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:50688800-50702600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:50689000-50693600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:50689200-50691800	Weak transcription	Fetal Intestine Small	intestine
44	chr3:50689200-50692000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:50689200-50692800	Weak transcription	Right Ventricle	heart
46	chr3:50689600-50690600	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr3:50690200-50692000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:50690200-50702200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:50690400-50691400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:50690400-50691600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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