Variant report

Variant	rs10019920
Chromosome Location	chr4:78866007-78866008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10005531	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10005935	0.81[CHB][hapmap]
rs10018117	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10026176	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10027634	0.83[EUR][1000 genomes]
rs10027739	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10030568	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10049674	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1106457	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11931471	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11931686	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11942975	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12509847	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13131331	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13131974	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1393643	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1587563	0.85[CHB][hapmap]
rs1604609	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17002804	0.85[CHB][hapmap]
rs2036455	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs2036457	0.92[CEU][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2088995	0.85[ASN][1000 genomes]
rs2102192	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28417234	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28436599	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28483318	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28685099	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4128860	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4328941	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4859512	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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]
rs4859882	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4859884	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4859890	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6533355	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6533372	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs67814821	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6814088	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6820725	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6835993	0.81[CHB][hapmap]
rs6849145	0.86[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7436080	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7660788	0.80[EUR][1000 genomes]
rs7682450	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs873280	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs924684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs924685	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9654194	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs9985806	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9994366	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10019920	MRPL1	cis	lymphoblastoid	seeQTL
rs10019920	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
2	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
4	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:78814600-78874400	Weak transcription	Pancreas	Pancrea
6	chr4:78816400-78866400	Weak transcription	Fetal Thymus	thymus
7	chr4:78816400-78876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr4:78816600-78875800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:78818800-78872800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:78821400-78873200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr4:78830000-78866600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:78830400-78877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:78844200-78871400	Weak transcription	NHDF-Ad	bronchial
14	chr4:78848800-78869000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:78849400-78876600	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:78849600-78871400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:78849600-78881000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:78850200-78881000	Weak transcription	A549	lung
19	chr4:78852000-78881200	Weak transcription	Lung	lung
20	chr4:78852600-78878200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:78853000-78874200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:78853200-78874600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr4:78853200-78878000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:78853200-78880800	Weak transcription	Osteobl	bone
25	chr4:78853200-78881000	Weak transcription	Brain Anterior Caudate	brain
26	chr4:78853400-78871600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:78853400-78873800	Weak transcription	NH-A	brain
28	chr4:78853400-78874600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:78853600-78871000	Weak transcription	Liver	Liver
30	chr4:78853600-78871400	Weak transcription	HepG2	liver
31	chr4:78853600-78872800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:78853800-78871200	Weak transcription	Fetal Lung	lung
33	chr4:78853800-78871400	Weak transcription	HUVEC	blood vessel
34	chr4:78853800-78876400	Weak transcription	Fetal Heart	heart
35	chr4:78853800-78877600	Weak transcription	NHEK	skin
36	chr4:78854000-78874400	Weak transcription	Fetal Intestine Large	intestine
37	chr4:78854200-78877800	Weak transcription	HSMMtube	muscle
38	chr4:78854800-78866400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr4:78856200-78871200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:78856400-78873600	Weak transcription	HSMM	muscle
41	chr4:78856800-78866600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr4:78858800-78871400	Weak transcription	Left Ventricle	heart
43	chr4:78858800-78871400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr4:78859400-78879000	Weak transcription	Small Intestine	intestine
45	chr4:78859600-78867600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:78860000-78866600	Weak transcription	Adipose Nuclei	Adipose
47	chr4:78860000-78877800	Weak transcription	Esophagus	oesophagus
48	chr4:78860400-78871000	Weak transcription	Ovary	ovary
49	chr4:78860400-78872800	Weak transcription	Aorta	Aorta
50	chr4:78860600-78866800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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