Variant report

Variant	rs4827
Chromosome Location	chr11:57507983-57507984
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57507517-57510599	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:57507932-57508363	GM12891	blood:	n/a	n/a
3	POLR2A	chr11:57507479-57513053	GM12878	blood:	n/a	n/a
4	POLR2A	chr11:57507778-57509843	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr11:57507456-57509881	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUN	chr11:57507756-57509891	K562	blood:	n/a	n/a
7	POLR2A	chr11:57507604-57509729	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr11:57507866-57510049	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr11:57507526-57510104	GM12892	blood:	n/a	n/a
10	POLR2A	chr11:57507744-57510228	GM12891	blood:	n/a	n/a
11	POLR2A	chr11:57507839-57509991	K562	blood:	n/a	n/a
12	POLR2A	chr11:57507698-57510489	GM12892	blood:	n/a	n/a
13	POLR2A	chr11:57507519-57510483	GM12892	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57440494..57443306-chr11:57507739..57511429,4	K562	blood:
2	chr11:57507833..57511012-chr11:57515890..57519512,4	MCF-7	breast:
3	chr11:57478095..57482223-chr11:57507421..57512003,5	K562	blood:
4	chr11:57434008..57435608-chr11:57507270..57509557,2	MCF-7	breast:
5	chr11:57478095..57481312-chr11:57507421..57511942,8	K562	blood:
6	chr11:57431371..57436913-chr11:57505728..57511660,10	K562	blood:
7	chr11:57478057..57480948-chr11:57506438..57510938,4	MCF-7	breast:
8	chr11:57507971..57508491-chr16:33956727..33957366,3	MCF-7	breast:
9	chr11:57434290..57436913-chr11:57507221..57510395,5	K562	blood:
10	chr11:57507427..57512619-chr11:57528805..57534217,7	K562	blood:
11	chr11:57478353..57481972-chr11:57506953..57510365,5	MCF-7	breast:

No data

Variant related genes	Relation type
C11orf31	TF binding region
ENSG00000254732	TF binding region
ENSG00000156599	Chromatin interaction
ENSG00000254462	Chromatin interaction
ENSG00000233436	Chromatin interaction
ENSG00000198561	Chromatin interaction
ENSG00000213593	Chromatin interaction
ENSG00000156603	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10792112	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896633	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896636	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896647	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11229113	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229116	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229130	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11229131	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11229148	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11570190	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11601320	0.81[EUR][1000 genomes]
rs11601449	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11602109	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11604325	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11604333	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11605731	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606396	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11607056	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12362166	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12785533	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12790196	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12804972	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12805841	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12807250	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1647405	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17455520	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2081361	0.83[AFR][1000 genomes]
rs2847308	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2926656	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35808061	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3781885	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs488769	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs499188	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs527528	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs543725	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs547891	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs576859	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs682503	0.81[EUR][1000 genomes]
rs708228	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7116341	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117205	0.81[EUR][1000 genomes]
rs7117878	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7121169	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7129727	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71484461	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71484468	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs731384	0.81[AFR][1000 genomes]
rs7932091	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7936998	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7938083	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7949841	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9420	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4827	MED19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57481000-57508400	Weak transcription	Aorta	Aorta
2	chr11:57481200-57508400	Weak transcription	Fetal Brain Male	brain
3	chr11:57481600-57508400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:57482000-57508200	Weak transcription	Brain Substantia Nigra	brain
5	chr11:57482200-57508200	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:57482400-57508000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:57482400-57508200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:57482400-57508200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr11:57482400-57508200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr11:57482600-57508000	Weak transcription	Small Intestine	intestine
11	chr11:57486000-57508400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:57492000-57508200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr11:57496600-57508400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:57500000-57508400	Weak transcription	HUVEC	blood vessel
15	chr11:57500200-57508000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:57500200-57508000	Strong transcription	Fetal Stomach	stomach
17	chr11:57500800-57508000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:57501600-57508000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr11:57501800-57508200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:57503000-57508200	Strong transcription	Fetal Muscle Trunk	muscle
21	chr11:57503400-57508400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr11:57504000-57508000	Weak transcription	Fetal Heart	heart
23	chr11:57504000-57508200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr11:57504000-57508400	Weak transcription	Stomach Mucosa	stomach
25	chr11:57504400-57508200	Strong transcription	NHEK	skin
26	chr11:57504800-57508000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:57504800-57508000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:57504800-57508000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr11:57505000-57508000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr11:57505000-57508000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:57505000-57508000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:57505000-57508000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr11:57505000-57508200	Strong transcription	A549	lung
34	chr11:57505000-57508200	Strong transcription	GM12878-XiMat	blood
35	chr11:57505200-57508000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr11:57505800-57508000	Strong transcription	Lung	lung
37	chr11:57505800-57508000	Genic enhancers	Dnd41	blood
38	chr11:57506000-57508000	Strong transcription	Fetal Intestine Small	intestine
39	chr11:57506200-57508200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:57506200-57508200	Weak transcription	HMEC	breast
41	chr11:57506400-57508000	Weak transcription	Spleen	Spleen
42	chr11:57506400-57508400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:57506600-57508000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr11:57506600-57508400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr11:57506800-57508000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr11:57506800-57508000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr11:57506800-57508200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:57506800-57508200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr11:57506800-57508200	Weak transcription	Primary B cells from cord blood	blood
50	chr11:57506800-57508200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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