Variant report

Variant	rs480933
Chromosome Location	chr11:57488160-57488161
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57488159-57488260	K562	blood:	n/a	n/a
2	POLR2A	chr11:57487930-57488294	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57483012..57485675-chr11:57487817..57489826,2	K562	blood:

Variant related genes	Relation type
ENSG00000213592	TF binding region

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10896634	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229087	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[ASN][1000 genomes]
rs11229115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267146	0.90[ASN][1000 genomes]
rs12793139	0.89[JPT][hapmap]
rs1424752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848445	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs479573	0.86[ASN][1000 genomes]
rs483030	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs486995	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491719	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492131	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501054	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501738	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503037	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs504311	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs504921	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs507946	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs509564	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs511708	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515939	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs517638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523985	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527140	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530094	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536673	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537627	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540234	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541245	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544446	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549022	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs549279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs558653	0.86[CEU][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567017	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs577741	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581217	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58132137	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs594233	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604094	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604344	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs608648	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs609596	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs612688	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61888873	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61888880	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624759	0.84[ASN][1000 genomes]
rs627816	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs628100	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636807	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs638864	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs640767	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs645097	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs647264	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs656227	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658183	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666021	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs669950	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs675154	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs676205	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs685110	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7108113	0.84[ASN][1000 genomes]
rs72928102	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs96894	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv975188	chr11:57480320-57494198	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs480933	SPRYD5	cis	cerebellum	SCAN
rs480933	MED19	cis	cerebellum	SCAN
rs480933	OR4C11	cis	cerebellum	SCAN
rs480933	MED19	cis	Artery Tibial	GTEx
rs480933	MED19	Cis_1M	lymphoblastoid	RTeQTL
rs480933	YPEL4	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57481000-57496200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:57481000-57508400	Weak transcription	Aorta	Aorta
3	chr11:57481200-57508400	Weak transcription	Fetal Brain Male	brain
4	chr11:57481400-57490800	Weak transcription	Stomach Mucosa	stomach
5	chr11:57481400-57496400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:57481400-57500200	Weak transcription	Esophagus	oesophagus
7	chr11:57481400-57503200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:57481400-57505000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:57481400-57506000	Weak transcription	Pancreas	Pancrea
10	chr11:57481600-57492000	Weak transcription	Right Atrium	heart
11	chr11:57481600-57505000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:57481600-57505000	Weak transcription	Fetal Kidney	kidney
13	chr11:57481600-57505000	Weak transcription	NH-A	brain
14	chr11:57481600-57506200	Weak transcription	Colonic Mucosa	Colon
15	chr11:57481600-57508400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:57481800-57496000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr11:57481800-57503000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:57481800-57503000	Weak transcription	HSMM	muscle
19	chr11:57481800-57505000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:57481800-57505000	Weak transcription	Fetal Lung	lung
21	chr11:57482000-57505000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr11:57482000-57505000	Weak transcription	NHLF	lung
23	chr11:57482000-57505200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr11:57482000-57505200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:57482000-57508200	Weak transcription	Brain Substantia Nigra	brain
26	chr11:57482200-57495200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:57482200-57496000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:57482200-57496400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr11:57482200-57498000	Weak transcription	HUVEC	blood vessel
30	chr11:57482200-57505000	Weak transcription	Brain Anterior Caudate	brain
31	chr11:57482200-57505000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr11:57482200-57505200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:57482200-57508200	Weak transcription	Colon Smooth Muscle	Colon
34	chr11:57482400-57494200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr11:57482400-57496000	Weak transcription	Brain Hippocampus Middle	brain
36	chr11:57482400-57500400	Weak transcription	Hela-S3	cervix
37	chr11:57482400-57503000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr11:57482400-57504800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:57482400-57505000	Weak transcription	Brain Angular Gyrus	brain
40	chr11:57482400-57508000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr11:57482400-57508200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:57482400-57508200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:57482400-57508200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:57482600-57492600	Weak transcription	A549	lung
45	chr11:57482600-57499800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:57482600-57503000	Weak transcription	Fetal Heart	heart
47	chr11:57482600-57508000	Weak transcription	Small Intestine	intestine
48	chr11:57482800-57499600	Weak transcription	Psoas Muscle	Psoas
49	chr11:57485000-57495000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:57485200-57488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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