Variant report

Variant	rs491719
Chromosome Location	chr11:57475520-57475521
allele	C/T
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	chr11:57475426-57475563	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57467968..57471169-chr11:57473477..57476394,3	MCF-7	breast:
2	chr11:57473781..57477362-chr11:57478566..57481637,6	K562	blood:

Variant related genes	Relation type
TMX2	TF binding region
TMX2-CTNND1	TF binding region
ENSG00000213593	Chromatin interaction
ENSG00000254462	Chromatin interaction
ENSG00000156603	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10896634	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229087	0.88[ASN][1000 genomes]
rs11229115	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1267146	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1424752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848445	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs479573	0.86[ASN][1000 genomes]
rs480933	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483030	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs486995	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs492131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501054	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501738	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503037	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs504311	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs504921	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs507946	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs509564	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511708	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515939	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs517638	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518804	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs523985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527140	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530094	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536673	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537627	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540234	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541245	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544446	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549022	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs549279	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs558653	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567017	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs577741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581217	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58132137	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs594233	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604094	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604344	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs608648	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs609596	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs612688	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61888873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61888880	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624759	0.84[ASN][1000 genomes]
rs627816	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs628100	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636807	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs638864	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs640767	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs645097	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs647264	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs656227	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658183	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666021	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669433	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs669950	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs675154	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs676205	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs685110	0.80[AMR][1000 genomes]
rs7108113	0.84[ASN][1000 genomes]
rs72928102	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs96894	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv975360	chr11:57466716-57480320	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs491719	MED19	Cis_1M	lymphoblastoid	RTeQTL
rs491719	MED19	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57436600-57479000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57438600-57478200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:57439000-57477400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:57448600-57476400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr11:57449000-57476000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:57458000-57475800	Strong transcription	Thymus	Thymus
7	chr11:57459200-57476200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:57461400-57478400	Weak transcription	Fetal Heart	heart
9	chr11:57464400-57478800	Weak transcription	Psoas Muscle	Psoas
10	chr11:57467600-57478200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:57468400-57478400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:57468400-57478800	Weak transcription	Right Ventricle	heart
13	chr11:57469000-57476000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr11:57469200-57478800	Weak transcription	Ovary	ovary
15	chr11:57469400-57478800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:57471400-57478000	Weak transcription	Primary B cells from cord blood	blood
17	chr11:57471800-57478400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr11:57472000-57477800	Weak transcription	K562	blood
19	chr11:57472000-57478400	Weak transcription	Fetal Kidney	kidney
20	chr11:57472000-57478600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:57472000-57478600	Weak transcription	Small Intestine	intestine
22	chr11:57472200-57477400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:57472200-57478400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:57472200-57478400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr11:57472400-57477600	Weak transcription	HUVEC	blood vessel
26	chr11:57472400-57478000	Weak transcription	Hela-S3	cervix
27	chr11:57472400-57478400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:57472400-57478400	Weak transcription	Brain Angular Gyrus	brain
29	chr11:57472600-57475800	Weak transcription	A549	lung
30	chr11:57472600-57477400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr11:57472600-57477400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr11:57472600-57477400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr11:57472600-57477400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:57472600-57477600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:57472600-57477600	Weak transcription	Colon Smooth Muscle	Colon
36	chr11:57472600-57477600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:57472600-57477600	Weak transcription	Lung	lung
38	chr11:57472600-57477600	Weak transcription	Pancreas	Pancrea
39	chr11:57472600-57477600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:57472600-57477600	Weak transcription	NHDF-Ad	bronchial
41	chr11:57472600-57478000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:57472600-57478000	Weak transcription	HSMM	muscle
43	chr11:57472600-57478200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:57472600-57478200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr11:57472600-57478200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr11:57472600-57478200	Weak transcription	Gastric	stomach
47	chr11:57472600-57478400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr11:57472600-57478400	Weak transcription	Brain Substantia Nigra	brain
49	chr11:57472600-57478400	Weak transcription	NHEK	skin
50	chr11:57472600-57478600	Weak transcription	Primary monocytes fromperipheralblood	blood

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