Variant report

Variant	rs2043293
Chromosome Location	chr19:19751456-19751457
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19750595-19751690	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:19751115-19751478	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:19751143-19751511	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:19751166-19751503	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:19751354-19751476	ProgFib	skin:	n/a	n/a
6	POLR2A	chr19:19751198-19751498	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:19750914-19751548	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19747528..19750723-chr19:19750885..19753735,4	MCF-7	breast:
2	chr19:19751259..19758144-chr19:19770384..19776332,14	K562	blood:
3	chr19:19749628..19752391-chr19:19752545..19755749,4	K562	blood:
4	chr19:19701585..19704571-chr19:19749702..19751858,2	K562	blood:
5	chr19:19751259..19757786-chr19:19771999..19776232,8	K562	blood:
6	chr19:19729069..19731549-chr19:19749818..19753000,3	MCF-7	breast:

No data

Variant related genes	Relation type
GMIP	TF binding region
ENSG00000105726	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000105717	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10403759	0.94[ASN][1000 genomes]
rs11878202	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11879838	0.93[ASN][1000 genomes]
rs12976826	0.94[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16994684	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16996174	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1968047	0.90[ASN][1000 genomes]
rs2304129	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34725331	0.92[ASN][1000 genomes]
rs4808974	0.94[ASN][1000 genomes]
rs7252228	0.92[ASN][1000 genomes]
rs739461	0.94[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8101679	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8113682	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs880090	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv911309	chr19:19727042-19784891	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2043293	UNC13A	cis	cerebellum	SCAN
rs2043293	MED26	cis	parietal	SCAN
rs2043293	GATAD2A	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19735000-19753200	Weak transcription	K562	blood
2	chr19:19738600-19753000	Weak transcription	Fetal Brain Male	brain
3	chr19:19738800-19752800	Weak transcription	Stomach Mucosa	stomach
4	chr19:19739800-19752600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:19739800-19753200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:19739800-19753400	Weak transcription	Small Intestine	intestine
7	chr19:19739800-19753400	Weak transcription	HMEC	breast
8	chr19:19739800-19753600	Weak transcription	Brain Angular Gyrus	brain
9	chr19:19739800-19753600	Weak transcription	Brain Substantia Nigra	brain
10	chr19:19739800-19753600	Weak transcription	Left Ventricle	heart
11	chr19:19739800-19753600	Weak transcription	Right Atrium	heart
12	chr19:19740000-19753400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:19740000-19753400	Weak transcription	Brain Anterior Caudate	brain
14	chr19:19740000-19753600	Weak transcription	Fetal Kidney	kidney
15	chr19:19740200-19753000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:19740400-19751600	Strong transcription	Brain Germinal Matrix	brain
17	chr19:19740400-19752600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:19740600-19751600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:19740800-19753000	Strong transcription	Fetal Stomach	stomach
20	chr19:19741000-19752600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:19742200-19752600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:19743200-19751600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:19745400-19753200	Weak transcription	NHDF-Ad	bronchial
24	chr19:19745600-19753200	Weak transcription	Hela-S3	cervix
25	chr19:19745600-19753400	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:19745600-19753400	Weak transcription	HUVEC	blood vessel
27	chr19:19745800-19753200	Weak transcription	HepG2	liver
28	chr19:19745800-19753400	Weak transcription	A549	lung
29	chr19:19745800-19753600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr19:19746200-19753400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr19:19746400-19751600	Strong transcription	GM12878-XiMat	blood
32	chr19:19746400-19752200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:19746400-19752200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:19746400-19753000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr19:19746400-19753600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:19746600-19752000	Strong transcription	Primary B cells from peripheral blood	blood
37	chr19:19746600-19752600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:19746600-19752800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr19:19746600-19753000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:19746600-19753200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:19746600-19753200	Weak transcription	Brain Hippocampus Middle	brain
42	chr19:19746600-19753200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr19:19746600-19753200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr19:19746600-19753400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr19:19746600-19753400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr19:19746600-19753400	Weak transcription	HSMMtube	muscle
47	chr19:19746600-19753600	Weak transcription	Fetal Intestine Large	intestine
48	chr19:19746600-19753600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr19:19746600-19753800	Weak transcription	Aorta	Aorta
50	chr19:19746600-19753800	Weak transcription	Ovary	ovary

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