Variant report

Variant	rs616689
Chromosome Location	chr3:50668532-50668533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50667896..50669989-chr3:50679232..50681112,3	K562	blood:
2	chr3:50666617..50668996-chr3:50683864..50686191,2	MCF-7	breast:
3	chr3:50653782..50659891-chr3:50667242..50673193,6	K562	blood:

Variant related genes	Relation type
ENSG00000114738	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1013233	0.83[AFR][1000 genomes]
rs1077215	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs1107312	0.85[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap]
rs11712367	0.82[CHD][hapmap];0.82[LWK][hapmap]
rs12486143	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12486717	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12487817	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12487821	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs12489607	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491812	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12492093	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492540	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12492982	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12494094	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12494326	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12495399	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[ASN][1000 genomes]
rs1385025	0.81[AFR][1000 genomes]
rs17050991	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17050995	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17051000	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17051043	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17051045	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17051403	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17051468	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs175634	0.83[CHD][hapmap]
rs1872184	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1971976	0.81[AFR][1000 genomes]
rs201193	0.84[AFR][1000 genomes]
rs2035484	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[ASN][1000 genomes]
rs2076927	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2170840	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227292	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2227293	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2239750	0.93[ASN][1000 genomes]
rs2239751	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239752	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2239753	0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2269505	0.96[LWK][hapmap];0.87[MKK][hapmap];0.80[AFR][1000 genomes]
rs2285090	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34848480	0.82[AFR][1000 genomes]
rs3749265	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3752449	0.93[ASN][1000 genomes]
rs375544	0.82[CHD][hapmap];0.96[LWK][hapmap];0.91[MKK][hapmap];0.87[AFR][1000 genomes]
rs3792323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3792325	0.85[AFR][1000 genomes]
rs3792328	0.82[CHD][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.87[AFR][1000 genomes]
rs3804627	0.96[LWK][hapmap];0.87[MKK][hapmap]
rs3804632	0.88[AFR][1000 genomes]
rs3806706	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs3943212	0.81[AFR][1000 genomes]
rs396302	0.96[LWK][hapmap];0.92[MKK][hapmap];0.88[AFR][1000 genomes]
rs443436	0.85[AFR][1000 genomes]
rs4476497	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs448028	0.88[AFR][1000 genomes]
rs4485709	0.82[CHD][hapmap]
rs453570	0.81[CHD][hapmap];0.85[MKK][hapmap];0.83[AFR][1000 genomes]
rs4640555	0.85[ASN][1000 genomes]
rs4688696	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs4688705	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]
rs4688707	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4688709	0.93[ASN][1000 genomes]
rs4688710	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4688713	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4688715	0.82[ASN][1000 genomes]
rs4688716	0.82[ASN][1000 genomes]
rs56170012	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56856095	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57910827	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58427389	0.98[ASN][1000 genomes]
rs58529408	0.87[ASN][1000 genomes]
rs59036236	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60552073	0.81[AMR][1000 genomes]
rs60877431	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs609678	0.93[YRI][hapmap]
rs61193866	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61316441	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61574029	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61613532	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs616589	0.87[AFR][1000 genomes]
rs6446208	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6446212	0.82[CHD][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.81[AFR][1000 genomes]
rs6446213	0.82[CHD][hapmap];0.82[LWK][hapmap]
rs6446222	0.81[CHD][hapmap];0.82[LWK][hapmap]
rs650655	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs667894	0.93[YRI][hapmap]
rs6766638	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6771348	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];0.97[ASN][1000 genomes]
rs6779819	0.82[CHD][hapmap];0.81[LWK][hapmap]
rs6783922	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794155	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796769	0.82[CHD][hapmap];0.81[LWK][hapmap]
rs728901	0.83[AFR][1000 genomes]
rs728902	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72938758	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs72942785	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72942794	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72944726	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72944730	0.87[ASN][1000 genomes]
rs73835531	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs743753	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs745356	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];0.97[ASN][1000 genomes]
rs751851	0.82[AFR][1000 genomes]
rs7615703	0.82[CHD][hapmap];0.82[LWK][hapmap]
rs762889	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs7646236	0.91[LWK][hapmap];0.92[MKK][hapmap];0.81[AFR][1000 genomes]
rs808148	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];0.97[ASN][1000 genomes]
rs808149	0.83[AFR][1000 genomes]
rs813243	0.82[CHD][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.85[AFR][1000 genomes]
rs876103	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]
rs876104	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][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]
rs876105	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]
rs900735	0.83[AFR][1000 genomes]
rs9682401	0.83[AFR][1000 genomes]
rs9814874	0.85[CHB][hapmap]
rs9825535	0.82[CHD][hapmap]
rs9868889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9869945	0.82[CHD][hapmap];0.82[LWK][hapmap]
rs9879397	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][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]

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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs616689	HEMK1	cis	multi-tissue	Pritchard
rs616689	HEMK1	cis	lymphoblastoid	seeQTL
rs616689	MAPKAPK3	cis	lymphoblastoid	seeQTL
rs616689	TUSC4	cis	Liver	GTEx
rs616689	TUSC4	cis	multi-tissue	Pritchard
rs616689	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:108 , 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	chr3:50656000-50675600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:50656000-50677800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:50657600-50678200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:50658400-50669000	Strong transcription	Fetal Stomach	stomach
7	chr3:50660200-50671600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:50660200-50677000	Weak transcription	Liver	Liver
9	chr3:50661200-50668800	Strong transcription	Fetal Intestine Small	intestine
10	chr3:50661400-50671600	Enhancers	Left Ventricle	heart
11	chr3:50661600-50670600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:50661600-50674400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:50661600-50675800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:50661600-50688200	Weak transcription	Small Intestine	intestine
15	chr3:50661800-50669000	Strong transcription	Fetal Intestine Large	intestine
16	chr3:50662000-50668600	Genic enhancers	Spleen	Spleen
17	chr3:50662200-50669000	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr3:50662400-50670000	Weak transcription	Fetal Lung	lung
19	chr3:50662400-50671000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:50662400-50672000	Enhancers	Primary hematopoietic stem cells	blood
21	chr3:50662400-50678200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:50662600-50675800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr3:50663200-50669200	Genic enhancers	Fetal Thymus	thymus
24	chr3:50663200-50677600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:50663400-50668600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:50663400-50690000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:50663800-50669200	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:50664000-50669000	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:50664200-50669600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr3:50664200-50672600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:50664400-50672800	Genic enhancers	Dnd41	blood
32	chr3:50665000-50668600	Enhancers	Right Ventricle	heart
33	chr3:50665200-50669200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:50665200-50674400	Weak transcription	Colonic Mucosa	Colon
35	chr3:50665400-50668600	Genic enhancers	Esophagus	oesophagus
36	chr3:50665400-50671000	Genic enhancers	NHEK	skin
37	chr3:50665400-50671200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:50665400-50679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:50665400-50686800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr3:50665600-50669000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:50665600-50669400	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:50665600-50670000	Weak transcription	Adipose Nuclei	Adipose
43	chr3:50665600-50673800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:50665600-50675600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:50665600-50686200	Weak transcription	Stomach Mucosa	stomach
46	chr3:50665800-50668600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:50665800-50669200	Weak transcription	Osteobl	bone
48	chr3:50665800-50669800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:50665800-50670200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:50665800-50670400	Weak transcription	Brain Inferior Temporal Lobe	brain

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