Variant report

Variant	rs507946
Chromosome Location	chr11:57589121-57589122
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10896634	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11229087	0.82[ASN][1000 genomes]
rs11229115	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1267146	0.83[ASN][1000 genomes]
rs1424752	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2848445	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs479573	0.81[ASN][1000 genomes]
rs480933	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs483030	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs486995	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs491719	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs492131	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs501054	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs501738	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs503037	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs504311	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs504921	0.81[EUR][1000 genomes]
rs509564	0.90[ASN][1000 genomes]
rs511708	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs515939	0.86[ASN][1000 genomes]
rs517638	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs518804	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs523985	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs527140	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs530094	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs536673	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs537627	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs540234	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs541245	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs544446	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs549022	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs549279	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs558653	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs567017	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs577741	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs580223	0.81[EUR][1000 genomes]
rs581217	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58132137	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs594233	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604094	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604344	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs608648	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609596	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs612688	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61888873	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61888880	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs624759	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs627816	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs628100	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs636807	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs638864	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs640767	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645097	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs647264	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs656227	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs658183	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs666021	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs669433	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs669950	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs675154	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs676205	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs685110	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs694131	0.88[EUR][1000 genomes]
rs694261	0.88[EUR][1000 genomes]
rs72928102	0.87[EUR][1000 genomes]
rs96894	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs507946	MED19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57569000-57589200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:57576000-57590600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:57579600-57604400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:57584600-57591000	Weak transcription	Primary B cells from cord blood	blood
5	chr11:57584800-57591400	Weak transcription	HMEC	breast
6	chr11:57584800-57591800	Weak transcription	A549	lung
7	chr11:57584800-57600600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:57585000-57589400	Weak transcription	Pancreas	Pancrea
9	chr11:57585000-57590400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr11:57585000-57591400	Weak transcription	Lung	lung
11	chr11:57585000-57591400	Weak transcription	Ovary	ovary
12	chr11:57585200-57591000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr11:57585200-57591400	Weak transcription	Brain Angular Gyrus	brain
14	chr11:57585400-57590200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:57585800-57589400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr11:57585800-57590000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:57585800-57590000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr11:57585800-57590000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:57585800-57590000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:57585800-57591200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:57585800-57591200	Weak transcription	Fetal Stomach	stomach
22	chr11:57585800-57591400	Weak transcription	Esophagus	oesophagus
23	chr11:57585800-57591400	Weak transcription	Left Ventricle	heart
24	chr11:57585800-57591800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr11:57586000-57590800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:57586000-57591200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:57586400-57589600	Weak transcription	Colonic Mucosa	Colon
28	chr11:57586400-57591000	Weak transcription	Adipose Nuclei	Adipose
29	chr11:57586600-57589400	Weak transcription	Placenta	Placenta
30	chr11:57586600-57592400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr11:57587000-57590000	Weak transcription	NHEK	skin
32	chr11:57587200-57589400	Weak transcription	Fetal Intestine Small	intestine
33	chr11:57587200-57589800	Weak transcription	Fetal Lung	lung
34	chr11:57587200-57589800	Weak transcription	NHDF-Ad	bronchial
35	chr11:57587200-57590600	Weak transcription	Osteobl	bone
36	chr11:57587200-57591400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:57587200-57594600	Weak transcription	HSMMtube	muscle
38	chr11:57587200-57597200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr11:57587400-57590200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr11:57587400-57590200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr11:57587400-57600600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:57587800-57590600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:57587800-57590600	Weak transcription	Fetal Intestine Large	intestine
44	chr11:57587800-57593000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:57587800-57593200	Weak transcription	HUVEC	blood vessel
46	chr11:57588000-57590400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:57588200-57591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:57588600-57590800	Weak transcription	Fetal Muscle Leg	muscle
49	chr11:57588800-57590400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr11:57588800-57591400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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