Variant report

Variant	rs3792323
Chromosome Location	chr3:50660331-50660332
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50653400..50656084-chr3:50660085..50663338,4	K562	blood:
2	chr3:50654232..50656084-chr3:50659888..50663338,3	K562	blood:
3	chr3:50656743..50658833-chr3:50659825..50662779,2	K562	blood:
4	chr3:50658545..50662764-chr3:50665293..50666982,3	K562	blood:
5	chr3:50659242..50661320-chr3:51428510..51430443,2	MCF-7	breast:
6	chr3:50658918..50663131-chr3:50672291..50676051,5	K562	blood:
7	chr3:50656064..50658112-chr3:50660024..50661781,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction
ENSG00000179837	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1077215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1107312	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12486143	0.82[ASN][1000 genomes]
rs12486717	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12487817	0.85[ASN][1000 genomes]
rs12487821	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs12489607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12491440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12491812	0.84[ASN][1000 genomes]
rs12492093	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12492540	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12492982	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12494094	0.86[ASN][1000 genomes]
rs12494326	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12495399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs17050991	0.84[ASN][1000 genomes]
rs17050995	0.85[ASN][1000 genomes]
rs17051000	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17051043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17051045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17051403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs1872184	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1894459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2035484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[ASN][1000 genomes]
rs2076927	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2170840	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2227292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2227293	0.94[ASN][1000 genomes]
rs2239750	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2239751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2239752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2239753	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2285090	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3749265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3752449	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3792325	0.84[CHB][hapmap]
rs3806706	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs396302	0.82[CHB][hapmap]
rs441516	0.82[CHB][hapmap]
rs4476497	0.95[ASN][1000 genomes]
rs4640555	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4688696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs4688705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4688707	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4688709	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4688710	0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4688713	0.82[ASN][1000 genomes]
rs4688715	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4688716	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56170012	0.87[ASN][1000 genomes]
rs56856095	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57591074	1.00[EUR][1000 genomes]
rs57910827	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58427389	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58529408	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59036236	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs60552073	0.81[ASN][1000 genomes]
rs60877431	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61193866	0.83[ASN][1000 genomes]
rs61316441	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61557316	1.00[EUR][1000 genomes]
rs61574029	0.84[ASN][1000 genomes]
rs61613532	0.85[ASN][1000 genomes]
rs616589	0.84[CHB][hapmap]
rs616689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6446208	0.91[ASN][1000 genomes]
rs650655	0.94[ASN][1000 genomes]
rs6766638	0.82[ASN][1000 genomes]
rs6771348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6783922	0.95[ASN][1000 genomes]
rs6794155	0.90[ASN][1000 genomes]
rs728902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72938758	0.85[ASN][1000 genomes]
rs72942760	0.82[AFR][1000 genomes]
rs72942785	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72942794	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72944726	0.85[ASN][1000 genomes]
rs72944730	0.85[ASN][1000 genomes]
rs73835531	0.84[ASN][1000 genomes]
rs743753	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs745356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs762889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs808148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs876103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs876104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs876105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9814874	0.84[CHB][hapmap]
rs9826757	0.86[CHB][hapmap]
rs9868889	0.95[ASN][1000 genomes]
rs9879397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
3	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
4	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
5	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
6	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
7	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
rs3792323	HEMK	cis	multi-tissue	Pritchard
rs3792323	HEMK1	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50655400-50677800	Weak transcription	Aorta	Aorta
2	chr3:50655600-50681200	Weak transcription	Fetal Brain Female	brain
3	chr3:50655800-50661000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:50655800-50661400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:50655800-50661400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:50655800-50661400	Weak transcription	Fetal Brain Male	brain
7	chr3:50655800-50661400	Weak transcription	NHLF	lung
8	chr3:50655800-50661600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:50655800-50661600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:50655800-50661600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:50655800-50661600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:50655800-50661800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:50655800-50661800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:50655800-50662000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:50655800-50662000	Weak transcription	Fetal Lung	lung
16	chr3:50655800-50662200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:50655800-50665000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:50655800-50665000	Weak transcription	Brain Angular Gyrus	brain
19	chr3:50655800-50666000	Enhancers	Fetal Heart	heart
20	chr3:50656000-50661200	Weak transcription	Small Intestine	intestine
21	chr3:50656000-50661400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:50656000-50675600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:50656000-50677800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:50656200-50661400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:50656800-50660600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:50656800-50664200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:50657200-50661000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:50657400-50661400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:50657400-50661400	Weak transcription	HepG2	liver
30	chr3:50657400-50661400	Genic enhancers	HMEC	breast
31	chr3:50657400-50662200	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:50657600-50660400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr3:50657600-50661400	Genic enhancers	Fetal Thymus	thymus
34	chr3:50657600-50678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:50658200-50661000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr3:50658200-50661000	Weak transcription	Pancreas	Pancrea
37	chr3:50658200-50661200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:50658200-50661200	Weak transcription	Adipose Nuclei	Adipose
39	chr3:50658200-50661400	Weak transcription	Hela-S3	cervix
40	chr3:50658200-50662600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:50658200-50662800	Weak transcription	Fetal Kidney	kidney
42	chr3:50658200-50663200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:50658400-50660400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:50658400-50660800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:50658400-50661000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:50658400-50661000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:50658400-50661000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:50658400-50661000	Weak transcription	Spleen	Spleen
49	chr3:50658400-50661200	Weak transcription	HSMMtube	muscle
50	chr3:50658400-50661400	Weak transcription	Colonic Mucosa	Colon

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