Variant report

Variant	rs523985
Chromosome Location	chr11:57481336-57481337
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr11:57478908-57481423	Hela-S3	cervix:	n/a	n/a
2	WRNIP1	chr11:57479691-57481391	GM12878	blood:	n/a	n/a
3	HEY1	chr11:57481173-57481429	K562	blood:	n/a	n/a
4	TAL1	chr11:57481324-57481629	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57296138..57298827-chr11:57479075..57481840,2	K562	blood:
2	chr11:57478353..57481972-chr11:57506953..57510365,5	MCF-7	breast:
3	chr11:57480551..57482263-chr11:57512925..57515700,2	K562	blood:
4	chr11:57433212..57437810-chr11:57477098..57481918,8	MCF-7	breast:
5	chr11:57481010..57482984-chr11:57566572..57568225,2	K562	blood:
6	chr11:57478095..57482223-chr11:57507421..57512003,5	K562	blood:
7	chr11:57433936..57437289-chr11:57477964..57482818,9	K562	blood:
8	chr11:57433884..57439071-chr11:57477629..57483930,15	K562	blood:

No data

Variant related genes	Relation type
MED19	TF binding region
ENSG00000134809	Chromatin interaction
ENSG00000156599	Chromatin interaction
ENSG00000211450	Chromatin interaction
ENSG00000254732	Chromatin interaction

Extended variants
information (count: 71 )
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];0.94[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];0.94[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2848445	0.80[AMR][1000 genomes];0.84[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483030	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs486995	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs492131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501054	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501738	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503037	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs504311	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs504921	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs507946	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs509564	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511708	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[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];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518804	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527140	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530094	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536673	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537627	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540234	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541245	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544446	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549022	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs549279	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs558653	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567017	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs577741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581217	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58132137	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs594233	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604094	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs604344	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs608648	0.86[AMR][1000 genomes];0.84[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];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61888873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61888880	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[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];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636807	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs638864	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs640767	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs645097	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs647264	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs656227	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs658183	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs666021	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs669433	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs669950	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs675154	0.86[AMR][1000 genomes];0.84[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];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs96894	0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs523985	MED19	Cis_1M	lymphoblastoid	RTeQTL
rs523985	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	chr11:57478400-57481800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr11:57478600-57481400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr11:57478600-57481600	Active TSS	K562	blood
4	chr11:57478600-57481800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr11:57478800-57482000	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr11:57478800-57482400	Active TSS	GM12878-XiMat	blood
7	chr11:57479000-57481600	Active TSS	Right Ventricle	heart
8	chr11:57479200-57481400	Active TSS	Esophagus	oesophagus
9	chr11:57479200-57481600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:57479200-57481600	Active TSS	Right Atrium	heart
11	chr11:57480200-57481400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr11:57480200-57481400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr11:57480200-57481400	Transcr. at gene 5' and 3'	Dnd41	blood
14	chr11:57480200-57481600	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr11:57480400-57481400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr11:57480400-57481400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr11:57480400-57481400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr11:57480400-57481400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:57480400-57481400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr11:57480400-57481400	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr11:57480400-57481400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr11:57480400-57481400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr11:57480400-57481800	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr11:57480400-57481800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr11:57480400-57481800	Flanking Active TSS	Liver	Liver
26	chr11:57480600-57481400	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr11:57480600-57481400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr11:57480600-57481400	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr11:57480600-57481400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr11:57480600-57481400	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr11:57480600-57481400	Enhancers	Spleen	Spleen
32	chr11:57480600-57481400	Flanking Active TSS	HUVEC	blood vessel
33	chr11:57480600-57481600	Flanking Active TSS	Fetal Lung	lung
34	chr11:57480600-57481800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr11:57480600-57481800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:57480600-57481800	Flanking Active TSS	Fetal Brain Female	brain
37	chr11:57480600-57481800	Flanking Active TSS	Thymus	Thymus
38	chr11:57480600-57482000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr11:57480600-57482000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:57480600-57482000	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr11:57480600-57482000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr11:57480600-57482200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr11:57480600-57482200	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr11:57480800-57481400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:57480800-57481400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:57480800-57481400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr11:57480800-57481400	Flanking Active TSS	Colonic Mucosa	Colon
48	chr11:57480800-57481400	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr11:57480800-57481400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr11:57480800-57481400	Flanking Active TSS	Fetal Heart	heart

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