Variant report

Variant	rs728902
Chromosome Location	chr3:50695362-50695363
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50654385..50656768-chr3:50694279..50695803,2	K562	blood:
2	chr3:50690938..50693728-chr3:50694642..50698811,4	K562	blood:
3	chr3:50682460..50684800-chr3:50693637..50696146,2	K562	blood:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1077215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1107312	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs12486143	0.85[AMR][1000 genomes]
rs12486717	0.89[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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12489607	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]
rs12491440	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492982	0.89[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]
rs12495399	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs17050991	0.88[AMR][1000 genomes]
rs17050995	0.85[AMR][1000 genomes]
rs17051000	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes]
rs17051043	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]
rs17051045	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]
rs17051403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[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]
rs1872184	0.89[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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2076927	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2170840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227292	1.00[CHB][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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239752	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2239753	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2285090	1.00[CHB][hapmap];1.00[JPT][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]
rs3792323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3806706	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs4476497	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688695	0.83[AFR][1000 genomes]
rs4688696	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
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	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4688709	0.87[ASN][1000 genomes]
rs4688710	0.95[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	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57910827	0.96[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	1.00[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[ASN][1000 genomes]
rs60602904	0.80[ASN][1000 genomes]
rs60877431	0.96[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	0.93[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[JPT][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]
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]
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]
rs72938758	0.87[AMR][1000 genomes]
rs72940708	0.83[EUR][1000 genomes]
rs72942785	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72942794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72944726	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72944730	0.85[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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[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]
rs762889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs808148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
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[JPT][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	0.86[CHB][hapmap]
rs9868889	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9879397	1.00[CHB][hapmap];1.00[JPT][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs728902	HEMK1	cis	multi-tissue	Pritchard
rs728902	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50670400-50699800	Weak transcription	Hela-S3	cervix
2	chr3:50685800-50703800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:50687000-50696400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:50687000-50712000	Weak transcription	Right Atrium	heart
5	chr3:50687400-50695600	Weak transcription	HMEC	breast
6	chr3:50687600-50697400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:50687600-50702400	Weak transcription	Spleen	Spleen
8	chr3:50688200-50702600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:50688800-50702600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:50690200-50702200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:50690400-50700200	Weak transcription	Left Ventricle	heart
12	chr3:50692800-50695600	Weak transcription	HSMM	muscle
13	chr3:50692800-50700600	Weak transcription	NHDF-Ad	bronchial
14	chr3:50693000-50695600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:50693000-50695600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:50693000-50695600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:50693000-50695600	Weak transcription	NHEK	skin
18	chr3:50693200-50695800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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