Variant report

Variant	rs12793139
Chromosome Location	chr11:57413943-57413944
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57413188-57413950	GM12892	blood:	n/a	n/a
2	EBF1	chr11:57413696-57414057	GM12878	blood:	n/a	chr11:57413943-57413954
3	CTCF	chr11:57413800-57413950	GM12873	blood:	n/a	n/a
4	RUNX3	chr11:57413574-57414053	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:57411937-57420676	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr11:57410796-57421100	H1-hESC	embryonic stem cell:	n/a	n/a
7	EBF1	chr11:57413751-57414110	GM12878	blood:	n/a	chr11:57413943-57413954
8	POLR2A	chr11:57412052-57419760	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr11:57404829-57418710	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr11:57410821-57420904	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr11:57412821-57416389	HUVEC	blood vessel:	n/a	n/a
12	SIN3A	chr11:57413866-57417706	H1-hESC	embryonic stem cell:	n/a	chr11:57414716-57414729 chr11:57416870-57416883 chr11:57415091-57415101 chr11:57417329-57417340
13	BHLHE40	chr11:57413841-57413961	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:57413864-57414896	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:57411926-57416336	HUVEC	blood vessel:	n/a	n/a
16	SMC3	chr11:57413842-57413999	GM12878	blood:	n/a	n/a
17	EP300	chr11:57413808-57413984	GM12878	blood:	n/a	n/a
18	MAZ	chr11:57413588-57414233	GM12878	blood:	n/a	n/a
19	RUNX3	chr11:57413594-57413989	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:57411980-57417263	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF7L2	chr11:57413808-57413991	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr11:57404802-57417187	SK-N-MC	brain:	n/a	n/a
23	POLR2A	chr11:57413693-57413968	A549	lung:	n/a	n/a
24	RELA	chr11:57413698-57414172	GM18951	blood:	n/a	n/a
25	POLR2A	chr11:57412040-57416702	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr11:57411922-57418069	SK-N-SH	brain:	n/a	n/a
27	ELF1	chr11:57413609-57413998	GM12878	blood:	n/a	n/a
28	POLR2A	chr11:57412961-57418210	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr11:57413929-57416256	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr11:57412201-57418679	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr11:57413511-57415806	PANC-1	pancreas:	n/a	n/a
32	POLR2A	chr11:57413876-57413948	ProgFib	skin:	n/a	n/a
33	POLR2A	chr11:57410100-57417938	PBDE	blood:	n/a	n/a
34	EP300	chr11:57413463-57413993	GM12878	blood:	n/a	n/a
35	ZNF143	chr11:57413850-57413962	GM12878	blood:	n/a	n/a
36	CTCF	chr11:57413840-57413990	SAEC	small airway:	n/a	n/a
37	EP300	chr11:57413773-57413952	GM12878	blood:	n/a	n/a
38	POLR2A	chr11:57413874-57415297	HUVEC	blood vessel:	n/a	n/a
39	EBF1	chr11:57413577-57414177	GM12878	blood:	n/a	chr11:57413943-57413954
40	POLR2A	chr11:57412996-57414001	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr11:57412737-57417005	U87	brain:	n/a	n/a
42	POLR2A	chr11:57412861-57418587	ECC-1	luminal epithelium:	n/a	n/a
43	TBP	chr11:57413108-57414152	GM12878	blood:	n/a	n/a
44	CHD2	chr11:57413898-57414131	GM12878	blood:	n/a	n/a
45	POLR2A	chr11:57412772-57417005	U87	brain:	n/a	n/a
46	POLR2A	chr11:57412977-57416985	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr11:57409804-57420281	PFSK-1	brain:	n/a	n/a
48	ATF2	chr11:57413560-57413948	H1-hESC	embryonic stem cell:	n/a	n/a
49	MXI1	chr11:57413407-57414058	GM12878	blood:	n/a	n/a
50	POLR2A	chr11:57413691-57413954	A549	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:57224684..57228396-chr11:57412206..57415806,3	K562	blood:
2	chr11:57335649..57336286-chr11:57413903..57414633,2	MCF-7	breast:
3	chr11:57191864..57193854-chr11:57413705..57415355,2	K562	blood:
4	chr11:57411538..57415148-chr11:57422707..57424942,3	K562	blood:
5	chr11:57090818..57092799-chr11:57412306..57413962,2	K562	blood:
6	chr11:57191864..57194047-chr11:57412922..57415205,2	K562	blood:
7	chr11:57333866..57335515-chr11:57412954..57415220,2	MCF-7	breast:

No data

Variant related genes	Relation type
CLP1	TF binding region
ENSG00000254602	TF binding region
ENSG00000134802	Chromatin interaction
ENSG00000186907	Chromatin interaction
ENSG00000156587	Chromatin interaction
ENSG00000149115	Chromatin interaction
ENSG00000172409	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1005510	0.81[CHB][hapmap]
rs1005511	0.81[CHB][hapmap]
rs11229087	0.91[CEU][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229115	0.81[JPT][hapmap]
rs1267146	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1424752	0.89[JPT][hapmap]
rs2511988	0.81[CHB][hapmap]
rs479573	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs480933	0.89[JPT][hapmap]
rs483030	0.89[JPT][hapmap]
rs501054	0.89[JPT][hapmap]
rs501738	0.82[JPT][hapmap]
rs503037	0.89[JPT][hapmap]
rs515939	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs518804	0.82[JPT][hapmap]
rs527140	0.89[JPT][hapmap]
rs530094	0.89[JPT][hapmap]
rs541245	0.89[JPT][hapmap]
rs544446	0.89[JPT][hapmap]
rs549022	0.89[JPT][hapmap]
rs567017	0.82[JPT][hapmap]
rs604344	0.89[JPT][hapmap]
rs669433	0.89[JPT][hapmap]
rs7108113	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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	esv992553	chr11:57408294-57419351	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12793139	MED19	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57409000-57414400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:57409000-57416200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:57409600-57414000	Weak transcription	Brain Germinal Matrix	brain
4	chr11:57410000-57414200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr11:57411000-57414600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
6	chr11:57411200-57414800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr11:57411200-57414800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:57411200-57415600	Enhancers	K562	blood
9	chr11:57411600-57414200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr11:57411600-57414200	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr11:57411600-57416200	Enhancers	Fetal Lung	lung
12	chr11:57412000-57414200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:57412000-57414200	Enhancers	Placenta	Placenta
14	chr11:57412000-57414200	Enhancers	Right Atrium	heart
15	chr11:57412000-57414400	Enhancers	Brain Anterior Caudate	brain
16	chr11:57412000-57414400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
17	chr11:57412000-57415800	Enhancers	Placenta Amnion	Placenta Amnion
18	chr11:57412200-57414200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:57412200-57414400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:57412200-57414400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:57412200-57414800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
22	chr11:57412200-57414800	Enhancers	HSMMtube	muscle
23	chr11:57412200-57415800	Enhancers	Ovary	ovary
24	chr11:57412200-57416200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:57412200-57416400	Bivalent Enhancer	Fetal Intestine Large	intestine
26	chr11:57412200-57416800	Enhancers	Lung	lung
27	chr11:57412200-57416800	Enhancers	Spleen	Spleen
28	chr11:57412200-57417000	Bivalent Enhancer	Stomach Mucosa	stomach
29	chr11:57412400-57414200	Weak transcription	Brain Substantia Nigra	brain
30	chr11:57412400-57414400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:57412600-57414200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr11:57412600-57414400	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr11:57412800-57414000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr11:57412800-57414000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr11:57412800-57414200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr11:57412800-57414200	Enhancers	Fetal Kidney	kidney
37	chr11:57412800-57414200	Bivalent Enhancer	HepG2	liver
38	chr11:57412800-57416000	Bivalent Enhancer	Fetal Thymus	thymus
39	chr11:57413000-57414400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:57413000-57414600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:57413000-57415000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
42	chr11:57413000-57415800	Enhancers	Fetal Brain Male	brain
43	chr11:57413000-57415800	Bivalent Enhancer	Rectal Smooth Muscle	rectum
44	chr11:57413000-57416400	Enhancers	Right Ventricle	heart
45	chr11:57413000-57416800	Bivalent Enhancer	NH-A	brain
46	chr11:57413200-57414000	Weak transcription	Brain Hippocampus Middle	brain
47	chr11:57413200-57414000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
48	chr11:57413200-57414200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:57413200-57414200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr11:57413200-57414800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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