Variant report

Variant	rs515939
Chromosome Location	chr11:57432629-57432630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57431371..57436913-chr11:57505728..57511660,10	K562	blood:
2	chr11:57281807..57284360-chr11:57431208..57434169,2	K562	blood:
3	chr11:57423095..57430151-chr11:57432283..57438412,24	K562	blood:

Variant related genes	Relation type
ENSG00000254732	Chromatin interaction
ENSG00000211450	Chromatin interaction
ENSG00000172409	Chromatin interaction
ENSG00000149150	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10896634	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11229087	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11229115	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1267146	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12793139	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1424752	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2848445	0.88[ASN][1000 genomes]
rs479573	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs480933	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs483030	0.89[ASN][1000 genomes]
rs486995	0.88[ASN][1000 genomes]
rs491719	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs492131	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs501054	0.89[ASN][1000 genomes]
rs501738	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs503037	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs504311	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs504921	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs507946	0.86[ASN][1000 genomes]
rs509564	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs511708	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs517638	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs518804	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs523985	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs527140	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs530094	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs536673	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs537627	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs540234	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs541245	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs544446	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs549022	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs549279	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs558653	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs567017	0.89[ASN][1000 genomes]
rs577741	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs581217	0.87[ASN][1000 genomes]
rs594233	0.89[ASN][1000 genomes]
rs604094	0.89[ASN][1000 genomes]
rs604344	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs608648	0.89[ASN][1000 genomes]
rs609596	0.83[ASN][1000 genomes]
rs612688	0.87[ASN][1000 genomes]
rs61888873	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61888880	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs624759	0.82[ASN][1000 genomes]
rs628100	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs636807	0.86[ASN][1000 genomes]
rs638864	0.89[ASN][1000 genomes]
rs640767	0.89[ASN][1000 genomes]
rs645097	0.87[ASN][1000 genomes]
rs647264	0.89[ASN][1000 genomes]
rs656227	0.89[ASN][1000 genomes]
rs658183	0.89[ASN][1000 genomes]
rs666021	0.86[ASN][1000 genomes]
rs669433	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs669950	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs675154	0.89[ASN][1000 genomes]
rs7108113	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[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	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs515939	MED19	Cis_1M	lymphoblastoid	RTeQTL
rs515939	MED19	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57426000-57434000	Weak transcription	Fetal Heart	heart
2	chr11:57426000-57434000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:57426000-57434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:57426000-57434200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:57427400-57434000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:57427600-57434000	Weak transcription	NHDF-Ad	bronchial
7	chr11:57428400-57434000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:57428400-57434200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:57428800-57434000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:57428800-57434200	Weak transcription	Fetal Brain Male	brain
11	chr11:57429000-57433600	Weak transcription	Hela-S3	cervix
12	chr11:57429000-57433800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:57429000-57433800	Weak transcription	Pancreas	Pancrea
14	chr11:57429000-57434000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr11:57429000-57434000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr11:57429000-57434000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:57429000-57434000	Weak transcription	A549	lung
18	chr11:57429000-57434200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr11:57429000-57434200	Weak transcription	Aorta	Aorta
20	chr11:57429000-57434200	Weak transcription	Esophagus	oesophagus
21	chr11:57429000-57434200	Weak transcription	Left Ventricle	heart
22	chr11:57429000-57434400	Weak transcription	Gastric	stomach
23	chr11:57429000-57434400	Weak transcription	Small Intestine	intestine
24	chr11:57429200-57433600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:57429200-57433800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr11:57429200-57433800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:57429200-57433800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:57429200-57433800	Weak transcription	HepG2	liver
29	chr11:57429200-57434000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:57429200-57434000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:57429200-57434000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr11:57429200-57434000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr11:57429200-57434000	Weak transcription	Psoas Muscle	Psoas
34	chr11:57429200-57434000	Weak transcription	NH-A	brain
35	chr11:57429200-57434200	Weak transcription	Brain Substantia Nigra	brain
36	chr11:57429200-57434200	Weak transcription	Colonic Mucosa	Colon
37	chr11:57429400-57433800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr11:57429400-57433800	Weak transcription	HMEC	breast
39	chr11:57429400-57434000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:57429400-57434000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr11:57429600-57434000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:57429600-57434200	Weak transcription	Ovary	ovary
43	chr11:57429800-57434000	Weak transcription	Fetal Intestine Small	intestine
44	chr11:57429800-57434000	Weak transcription	Right Ventricle	heart
45	chr11:57429800-57434200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:57430000-57433600	Weak transcription	Primary B cells from cord blood	blood
47	chr11:57430000-57433600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:57430000-57434000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr11:57430200-57433200	Weak transcription	Primary hematopoietic stem cells	blood
50	chr11:57430200-57433400	Weak transcription	Dnd41	blood

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