Variant report

Variant	rs3745779
Chromosome Location	chr19:37064032-37064033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:456)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:456 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr19:37063831-37064380	HepG2	liver:	n/a	n/a
2	HDAC2	chr19:37063926-37064205	K562	blood:	n/a	n/a
3	POLR2A	chr19:37063909-37064443	A549	lung:	n/a	n/a
4	NFATC1	chr19:37063841-37064323	GM12878	blood:	n/a	n/a
5	SMC3	chr19:37063846-37064141	HepG2	liver:	n/a	n/a
6	UBTF	chr19:37063886-37064797	K562	blood:	n/a	n/a
7	CHD2	chr19:37063849-37064522	HepG2	liver:	n/a	n/a
8	MAX	chr19:37063710-37064391	H1-hESC	embryonic stem cell:	n/a	n/a
9	MYC	chr19:37063888-37064285	HUVEC	blood vessel:	n/a	n/a
10	ETS1	chr19:37063837-37064525	GM12878	blood:	n/a	chr19:37064508-37064521
11	TAL1	chr19:37063866-37064364	K562	blood:	n/a	n/a
12	ELK4	chr19:37063959-37064433	HEK293	kidney:	n/a	n/a
13	USF1	chr19:37063757-37064227	A549	lung:	n/a	n/a
14	SIX5	chr19:37063543-37065034	A549	lung:	n/a	chr19:37064824-37064833
15	TBP	chr19:37063721-37064429	GM12878	blood:	n/a	n/a
16	ESR1	chr19:37064028-37064345	ECC-1	luminal epithelium:	n/a	chr19:37064156-37064171
17	PML	chr19:37063779-37064477	K562	blood:	n/a	n/a
18	RELA	chr19:37063715-37064447	GM18505	blood:	n/a	n/a
19	PML	chr19:37063888-37064504	K562	blood:	n/a	n/a
20	CTCF	chr19:37063885-37064418	GM12878	blood:	n/a	n/a
21	MAX	chr19:37063775-37064420	MCF-7	breast:	n/a	n/a
22	USF2	chr19:37063748-37064363	Hela-S3	cervix:	n/a	n/a
23	SP4	chr19:37063908-37064336	H1-hESC	embryonic stem cell:	n/a	chr19:37063925-37063941
24	RFX5	chr19:37063833-37064410	HepG2	liver:	n/a	n/a
25	HEY1	chr19:37063842-37064625	HepG2	liver:	n/a	n/a
26	MAX	chr19:37063674-37064511	ECC-1	luminal epithelium:	n/a	n/a
27	FOS	chr19:37063980-37064274	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr19:37063759-37064981	K562	blood:	n/a	n/a
29	GABPA	chr19:37063848-37064829	K562	blood:	n/a	n/a
30	CTCF	chr19:37063621-37064362	K562	blood:	n/a	n/a
31	TAF1	chr19:37063842-37064483	PFSK-1	brain:	n/a	n/a
32	BATF	chr19:37063960-37064323	GM12878	blood:	n/a	n/a
33	TAF1	chr19:37063705-37064809	H1-hESC	embryonic stem cell:	n/a	n/a
34	PAX5	chr19:37063972-37064346	GM12878	blood:	n/a	n/a
35	CHD2	chr19:37063778-37064431	K562	blood:	n/a	n/a
36	POLR2A	chr19:37063789-37064545	K562	blood:	n/a	n/a
37	USF1	chr19:37063963-37064259	K562	blood:	n/a	n/a
38	TCF3	chr19:37063885-37064488	GM12878	blood:	n/a	n/a
39	TCF7L2	chr19:37063831-37064296	PANC-1	pancreas:	n/a	n/a
40	MYC	chr19:37063850-37064266	MCF-7	breast:	n/a	n/a
41	NFATC1	chr19:37063838-37064452	GM12878	blood:	n/a	n/a
42	SIN3AK20	chr19:37063816-37064471	H1-hESC	embryonic stem cell:	n/a	n/a
43	RCOR1	chr19:37063790-37064989	K562	blood:	n/a	n/a
44	SIN3AK20	chr19:37063676-37064601	MCF-7	breast:	n/a	n/a
45	MYC	chr19:37063618-37064985	K562	blood:	n/a	chr19:37064538-37064548
46	GABPA	chr19:37063623-37064971	MCF-7	breast:	n/a	n/a
47	MYBL2	chr19:37063773-37064551	HepG2	liver:	n/a	n/a
48	CEBPB	chr19:37063967-37064147	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:37063721-37065130	K562	blood:	n/a	n/a
50	ZEB1	chr19:37064029-37064448	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:37017989..37021035-chr19:37064029..37066517,3	MCF-7	breast:
2	chr19:36979193..36981748-chr19:37061672..37065426,4	K562	blood:
3	chr19:36704361..36705921-chr19:37063810..37066277,2	K562	blood:
4	chr19:37019103..37021335-chr19:37062459..37064743,4	K562	blood:
5	chr19:37063014..37065659-chr19:37066533..37068326,2	MCF-7	breast:
6	chr1:144533722..144534489-chr19:37063772..37064389,2	Hela-S3	cervix:
7	chr19:37038594..37041681-chr19:37063019..37065867,3	K562	blood:
8	chr19:37063854..37065418-chr19:37262714..37265586,2	K562	blood:
9	chr19:36979379..36982047-chr19:37063909..37066157,2	K562	blood:
10	chr19:37062757..37066475-chr19:37067178..37075829,11	K562	blood:
11	chr19:37062757..37067111-chr19:37067178..37071986,8	K562	blood:
12	chr19:36940091..36943076-chr19:37061156..37065481,3	K562	blood:
13	chr19:37063664..37064432-chr3:73159959..73160622,2	Hela-S3	cervix:
14	chr1:153963085..153963674-chr19:37063863..37064467,2	Hela-S3	cervix:
15	chr19:37062686..37064573-chr19:37176993..37178796,2	MCF-7	breast:
16	chr1:249132382..249132990-chr19:37063673..37064639,2	Hela-S3	cervix:
17	chr19:37018711..37023188-chr19:37060299..37065354,5	K562	blood:
18	chr19:37037541..37041127-chr19:37063019..37065545,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092295.7.1-3	chr19:37063972-37064427	ENSG00000233527.4

No data

Variant related genes	Relation type
ENSG00000233527	TF binding region
ENSG00000225975	Chromatin interaction
ENSG00000171161	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000186017	Chromatin interaction
ENSG00000167635	Chromatin interaction
ENSG00000267041	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000228629	Chromatin interaction
ENSG00000267260	Chromatin interaction
ENSG00000267309	Chromatin interaction
ENSG00000189042	Chromatin interaction
ENSG00000196357	Chromatin interaction
ENSG00000223247	Chromatin interaction
ENSG00000254004	Chromatin interaction
ENSG00000177954	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10414896	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1234514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17238977	0.90[CEU][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2114287	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278168	0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2912401	0.85[TSI][hapmap]
rs2912402	0.85[TSI][hapmap]
rs2967470	0.87[TSI][hapmap]
rs3096621	0.81[CEU][hapmap]
rs3108176	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108177	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3108204	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108207	0.87[TSI][hapmap]
rs3108210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108216	0.94[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108548	0.82[TSI][hapmap]
rs3108551	0.84[TSI][hapmap]
rs3108556	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108558	0.87[TSI][hapmap]
rs3108561	0.87[TSI][hapmap]
rs3108578	0.84[TSI][hapmap]
rs3108612	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3170326	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3760826	0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56319939	0.90[AMR][1000 genomes]
rs57854762	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61259689	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61396420	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61732180	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112474	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112477	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62112481	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7254978	0.87[TSI][hapmap]
rs73034161	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7343133	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8111881	0.87[EUR][1000 genomes];0.86[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	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3334779	chr19:37050161-37076919	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3745779	TEX101	cis	cerebellum	SCAN
rs3745779	CEACAM20	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37062600-37065400	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr19:37062800-37064800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:37062800-37065000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:37062800-37065600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:37062800-37065600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:37062800-37065600	Active TSS	Colonic Mucosa	Colon
7	chr19:37062800-37065800	Active TSS	HMEC	breast
8	chr19:37062800-37066000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr19:37062800-37066000	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr19:37063000-37065200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:37063000-37065400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:37063000-37065400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:37063000-37065600	Active TSS	NHLF	lung
14	chr19:37063000-37065800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:37063000-37066000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr19:37063200-37065000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:37063200-37065000	Active TSS	HSMMtube	muscle
18	chr19:37063200-37065200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr19:37063200-37065200	Active TSS	Right Atrium	heart
20	chr19:37063200-37065400	Active TSS	Muscle Satellite Cultured Cells	--
21	chr19:37063200-37065400	Active TSS	Fetal Muscle Trunk	muscle
22	chr19:37063200-37065400	Active TSS	HSMM	muscle
23	chr19:37063200-37065600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:37063200-37065600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:37063200-37065600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:37063200-37065800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr19:37063200-37065800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:37063200-37065800	Active TSS	Rectal Smooth Muscle	rectum
29	chr19:37063200-37065800	Active TSS	Right Ventricle	heart
30	chr19:37063400-37064600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr19:37063400-37064600	Active TSS	A549	lung
32	chr19:37063400-37065000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:37063400-37065000	Active TSS	Brain Hippocampus Middle	brain
34	chr19:37063400-37065000	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr19:37063400-37065000	Active TSS	Left Ventricle	heart
36	chr19:37063400-37065000	Active TSS	Lung	lung
37	chr19:37063400-37065000	Bivalent/Poised TSS	HepG2	liver
38	chr19:37063400-37065000	Active TSS	Osteobl	bone
39	chr19:37063400-37065200	Active TSS	Aorta	Aorta
40	chr19:37063400-37065200	Active TSS	Fetal Thymus	thymus
41	chr19:37063400-37065200	Active TSS	Ovary	ovary
42	chr19:37063400-37065400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr19:37063400-37065400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:37063400-37065400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:37063400-37065400	Active TSS	Fetal Kidney	kidney
46	chr19:37063400-37065400	Active TSS	Pancreas	Pancrea
47	chr19:37063400-37065400	Active TSS	NH-A	brain
48	chr19:37063400-37065600	Active TSS	H9 Cell Line	embryonic stem cell
49	chr19:37063400-37065600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:37063400-37065600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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