Variant report

Variant	rs3787040
Chromosome Location	chr19:19297292-19297293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr19:19296716-19297723	K562	blood:	n/a	n/a
2	CHD2	chr19:19297000-19297513	K562	blood:	n/a	n/a
3	SPI1	chr19:19297012-19297716	HL-60	blood:	n/a	n/a
4	MAZ	chr19:19296652-19297357	IMR90	lung:	n/a	n/a
5	SPI1	chr19:19297221-19297479	HL-60	blood:	n/a	n/a
6	BHLHE40	chr19:19296840-19297409	K562	blood:	n/a	n/a
7	RAD21	chr19:19296482-19297353	SK-N-SH	brain:	n/a	n/a
8	RUNX3	chr19:19297172-19297467	GM12878	blood:	n/a	n/a
9	MAX	chr19:19296717-19297448	K562	blood:	n/a	n/a
10	POLR2A	chr19:19296554-19298034	K562	blood:	n/a	n/a
11	RAD21	chr19:19296579-19297322	HCT-116	colon:	n/a	n/a
12	POLR2A	chr19:19296653-19298053	HL-60	blood:	n/a	n/a
13	POLR2A	chr19:19296493-19297305	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr19:19296752-19297411	K562	blood:	n/a	n/a
15	MYC	chr19:19296845-19297311	K562	blood:	n/a	n/a
16	POLR2A	chr19:19296743-19297685	HL-60	blood:	n/a	n/a
17	ZBTB33	chr19:19297139-19297461	K562	blood:	n/a	n/a
18	CTCF	chr19:19296545-19297300	SK-N-SH	brain:	n/a	chr19:19296677-19296686

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19294693..19300778-chr19:19301483..19306941,9	K562	blood:
2	chr19:19296821..19298878-chr19:19300164..19303100,3	MCF-7	breast:
3	chr19:19291680..19293828-chr19:19294510..19298396,4	K562	blood:
4	chr19:19295305..19299616-chr19:19301493..19303729,7	K562	blood:
5	chr19:19296559..19297342-chr19:19453264..19453811,2	MCF-7	breast:

No data

Variant related genes	Relation type
MEF2BNB-MEF2B	TF binding region
MEF2BNB	TF binding region
ENSG00000064489	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000254901	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1005980	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10417796	0.82[EUR][1000 genomes]
rs10418053	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs1050544	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs10854008	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10854009	0.81[EUR][1000 genomes]
rs10854012	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11669408	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669860	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11669861	0.84[EUR][1000 genomes]
rs12609573	1.00[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12972894	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974672	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12975253	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12975290	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12980269	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12980955	0.81[EUR][1000 genomes]
rs12981160	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1858846	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2238668	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239369	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2239370	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2283623	0.81[EUR][1000 genomes]
rs2314035	0.82[EUR][1000 genomes]
rs35342977	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4808185	0.85[EUR][1000 genomes]
rs539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62135499	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71332145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7250650	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7256811	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7260127	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72997174	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs741706	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8101388	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833779	chr19:19163492-19313091	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv933613	chr19:19291456-19312244	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv961283	chr19:19293486-19312277	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3787040	C19orf50	cis	parietal	SCAN
rs3787040	ZNF682	cis	parietal	SCAN
rs3787040	PDE4C	cis	cerebellum	SCAN
rs3787040	C19orf50	cis	cerebellum	SCAN
rs3787040	RAB8A	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19277400-19300600	Weak transcription	Small Intestine	intestine
2	chr19:19280800-19301600	Weak transcription	NHEK	skin
3	chr19:19281400-19300800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:19281600-19299400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr19:19281600-19300600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:19281600-19302000	Weak transcription	NH-A	brain
7	chr19:19281600-19302200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:19281800-19300000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:19281800-19301200	Weak transcription	Stomach Mucosa	stomach
10	chr19:19282000-19301600	Weak transcription	Fetal Heart	heart
11	chr19:19283400-19300600	Weak transcription	Psoas Muscle	Psoas
12	chr19:19283400-19301600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:19283400-19302000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:19283400-19302200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr19:19283600-19301800	Weak transcription	HSMMtube	muscle
16	chr19:19284200-19302000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:19285600-19301800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr19:19286000-19301000	Weak transcription	HepG2	liver
19	chr19:19286000-19302000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr19:19286600-19298200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:19288600-19300600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:19289800-19300800	Weak transcription	NHDF-Ad	bronchial
23	chr19:19291200-19298000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr19:19291400-19298200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr19:19291400-19298200	Strong transcription	Fetal Stomach	stomach
26	chr19:19291400-19300800	Strong transcription	Fetal Intestine Small	intestine
27	chr19:19291600-19297800	Strong transcription	Placenta	Placenta
28	chr19:19291600-19298200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:19291800-19300000	Weak transcription	Colon Smooth Muscle	Colon
30	chr19:19291800-19301600	Weak transcription	A549	lung
31	chr19:19292200-19298000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:19292800-19301600	Weak transcription	HMEC	breast
33	chr19:19293000-19300800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr19:19293400-19297400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr19:19293400-19297600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:19293400-19300800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:19293400-19300800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr19:19293600-19297600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:19293600-19297800	Weak transcription	Right Ventricle	heart
40	chr19:19293600-19300000	Weak transcription	Brain Angular Gyrus	brain
41	chr19:19293600-19300200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr19:19293600-19300800	Weak transcription	Hela-S3	cervix
43	chr19:19293600-19301000	Weak transcription	Osteobl	bone
44	chr19:19293600-19301800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr19:19293600-19301800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:19293600-19301800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:19293600-19302000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr19:19293600-19302000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr19:19293600-19302200	Weak transcription	Aorta	Aorta
50	chr19:19293800-19297600	Weak transcription	Esophagus	oesophagus

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