Variant report

Variant	rs876103
Chromosome Location	chr3:50684011-50684012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50653198..50654878-chr3:50683228..50685763,2	MCF-7	breast:
2	chr3:50666617..50668996-chr3:50683864..50686191,2	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];0.94[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];0.94[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];0.98[ASN][1000 genomes]
rs12491440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12491812	0.89[AMR][1000 genomes]
rs12492093	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12492540	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12492982	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12494094	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12494326	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12495399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1385025	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];0.80[ASN][1000 genomes]
rs17051043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17051468	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1872184	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1894459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1971976	0.84[AFR][1000 genomes]
rs2035484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2076927	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[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];0.98[ASN][1000 genomes]
rs2227292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2227293	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2239750	0.88[ASN][1000 genomes]
rs2239751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2239752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2239753	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2285090	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34848480	0.86[AFR][1000 genomes]
rs3749265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3752449	0.88[ASN][1000 genomes]
rs375544	0.84[AFR][1000 genomes]
rs3792323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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	0.86[AFR][1000 genomes]
rs4476497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs448028	0.83[AFR][1000 genomes]
rs4640555	0.81[ASN][1000 genomes]
rs4688696	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4688705	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]
rs4688707	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4688709	0.88[ASN][1000 genomes]
rs4688710	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4688713	0.86[AMR][1000 genomes]
rs56170012	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56856095	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57910827	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58427389	0.97[ASN][1000 genomes]
rs58529408	0.90[ASN][1000 genomes]
rs59036236	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60552073	0.81[AMR][1000 genomes]
rs60552386	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];0.88[ASN][1000 genomes]
rs61574029	0.90[AMR][1000 genomes]
rs61613532	0.90[AMR][1000 genomes]
rs616589	0.80[JPT][hapmap];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];0.95[ASN][1000 genomes]
rs6446208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6446212	0.84[AFR][1000 genomes]
rs650655	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.98[ASN][1000 genomes]
rs6783922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6794155	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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];0.98[ASN][1000 genomes]
rs72938758	0.90[AMR][1000 genomes]
rs72942785	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72942794	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72944726	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72944730	0.90[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];0.91[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];0.98[ASN][1000 genomes]
rs751851	0.86[AFR][1000 genomes]
rs762889	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[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];0.98[ASN][1000 genomes]
rs808149	0.88[AFR][1000 genomes]
rs813243	0.81[AFR][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];0.98[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];0.98[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
rs876103	HEMK	cis	multi-tissue	Pritchard
rs876103	HEMK1	cis	multi-tissue	Pritchard

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50661600-50688200	Weak transcription	Small Intestine	intestine
2	chr3:50663400-50690000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:50665400-50686800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:50665600-50686200	Weak transcription	Stomach Mucosa	stomach
5	chr3:50669000-50684800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:50670200-50689000	Weak transcription	K562	blood
7	chr3:50670400-50699800	Weak transcription	Hela-S3	cervix
8	chr3:50672400-50688000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:50674200-50687200	Strong transcription	Dnd41	blood
10	chr3:50675400-50687400	Strong transcription	Thymus	Thymus
11	chr3:50675600-50684600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:50675800-50688000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:50676000-50686000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:50676000-50687600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr3:50676000-50688200	Strong transcription	Primary T cells from cord blood	blood
16	chr3:50676000-50689200	Strong transcription	Fetal Intestine Small	intestine
17	chr3:50676200-50686600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:50676200-50686600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr3:50676200-50686800	Strong transcription	Lung	lung
20	chr3:50676400-50686000	Strong transcription	Fetal Stomach	stomach
21	chr3:50676400-50686800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr3:50676400-50687000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:50676400-50687600	Strong transcription	Fetal Intestine Large	intestine
24	chr3:50676400-50688000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:50676400-50688000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:50676400-50688800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:50676600-50687600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:50676600-50688200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:50676800-50686800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:50676800-50687000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:50676800-50687200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:50676800-50688000	Strong transcription	Esophagus	oesophagus
33	chr3:50677000-50686400	Strong transcription	Fetal Thymus	thymus
34	chr3:50677000-50686800	Strong transcription	Liver	Liver
35	chr3:50677200-50685200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:50677200-50686200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:50677400-50686000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr3:50677400-50686200	Weak transcription	HSMMtube	muscle
39	chr3:50677400-50687400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:50677400-50687400	Strong transcription	HMEC	breast
41	chr3:50677400-50687600	Strong transcription	Primary hematopoietic stem cells	blood
42	chr3:50677400-50687600	Strong transcription	NHEK	skin
43	chr3:50677400-50692200	Weak transcription	NHDF-Ad	bronchial
44	chr3:50677600-50686600	Strong transcription	Placenta	Placenta
45	chr3:50677600-50686800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:50677600-50686800	Strong transcription	Gastric	stomach
47	chr3:50677800-50684400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:50677800-50685000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:50677800-50686000	Strong transcription	Colonic Mucosa	Colon
50	chr3:50677800-50686000	Strong transcription	Sigmoid Colon	Sigmoid Colon

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