Variant report

Variant	rs274156
Chromosome Location	chr19:56683450-56683451
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:56683190-56683598	HepG2	liver:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
2	RAD21	chr19:56683246-56683543	GM12878	blood:	n/a	chr19:56683414-56683427
3	EBF1	chr19:56683274-56683548	GM12878	blood:	n/a	n/a
4	CTCF	chr19:56683360-56683510	GM12873	blood:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
5	CTCF	chr19:56683360-56683510	Caco-2	colon:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
6	RAD21	chr19:56683220-56683617	GM12878	blood:	n/a	chr19:56683414-56683427
7	CTCF	chr19:56683340-56683490	GM12801	blood:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
8	REST	chr19:56683244-56683564	PFSK-1	brain:	n/a	chr19:56683376-56683389
9	CTCF	chr19:56683320-56683585	LNCaP	prostate:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
10	CTCF	chr19:56683245-56683565	A549	lung:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
11	JUND	chr19:56683317-56683582	K562	blood:	n/a	n/a
12	GTF2F1	chr19:56683284-56683519	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr19:56683340-56683490	NHDF-neo	bronchial:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
14	CTCF	chr19:56683380-56683530	AG09319	gingival:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
15	CTCF	chr19:56683420-56683570	HAc	cerebellar:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
16	MYC	chr19:56683305-56683507	K562	blood:	n/a	n/a
17	GABPA	chr19:56683207-56683543	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr19:56683360-56683510	GM12874	blood:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
19	BRCA1	chr19:56683440-56683540	HepG2	liver:	n/a	n/a
20	CTCF	chr19:56683400-56683550	GM12875	blood:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
21	CTCF	chr19:56683380-56683530	NHLF	lung:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
22	RAD21	chr19:56683210-56683671	HepG2	liver:	n/a	chr19:56683414-56683427
23	CTCF	chr19:56683243-56683642	K562	blood:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
24	CTCF	chr19:56683303-56683574	MCF-7	breast:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
25	CBX3	chr19:56683261-56683595	K562	blood:	n/a	n/a
26	CTCF	chr19:56683440-56683590	HFF-Myc	foreskin:	n/a	n/a
27	CTCF	chr19:56683303-56683593	MCF-7	breast:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
28	TAF7	chr19:56683250-56683526	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr19:56683360-56683510	A549	lung:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
30	CTCF	chr19:56683380-56683530	HCFaa	heart:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
31	RAD21	chr19:56683147-56683779	HCT-116	colon:	n/a	chr19:56683414-56683427
32	CEBPB	chr19:56683200-56683624	MCF-7	breast:	n/a	n/a
33	CTCF	chr19:56683274-56683623	ECC-1	luminal epithelium:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
34	CTCF	chr19:56683380-56683530	K562	blood:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
35	ELF1	chr19:56683233-56683548	GM12878	blood:	n/a	n/a
36	CTCF	chr19:56683340-56683490	HepG2	liver:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
37	CTCF	chr19:56683340-56683490	HEEpiC	esophagus:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
38	CTCF	chr19:56683380-56683530	HPF	lung:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
39	YY1	chr19:56683328-56683582	GM12878	blood:	n/a	n/a
40	CEBPB	chr19:56683258-56683477	K562	blood:	n/a	n/a
41	MAFF	chr19:56683366-56683515	HepG2	liver:	n/a	n/a
42	CEBPB	chr19:56683210-56683588	HepG2	liver:	n/a	n/a
43	CTCF	chr19:56683360-56683510	HUVEC	blood vessel:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
44	TBL1XR1	chr19:56683366-56683565	K562	blood:	n/a	n/a
45	CTCF	chr19:56683360-56683510	GM12871	blood:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
46	CTCF	chr19:56683246-56683644	IMR90	lung:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
47	CTCF	chr19:56683360-56683510	GM06990	blood:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
48	CTCF	chr19:56683340-56683490	GM12865	blood:	n/a	chr19:56683431-56683449 chr19:56683432-56683448
49	EGR1	chr19:56683270-56683542	H1-hESC	embryonic stem cell:	n/a	chr19:56683431-56683446
50	CTCF	chr19:56683332-56683569	HepG2	liver:	n/a	chr19:56683431-56683449 chr19:56683432-56683448

No.	Distal block	Cell Line	Cell type
1	chr19:56682699..56684265-chr19:56686805..56689043,2	K562	blood:
2	chr19:56587474..56588459-chr19:56682965..56683942,4	MCF-7	breast:
3	chr19:56616140..56616760-chr19:56683418..56683934,2	MCF-7	breast:
4	chr19:56616234..56617536-chr19:56682954..56683960,8	MCF-7	breast:
5	chr19:56666238..56667090-chr19:56683427..56683991,2	K562	blood:
6	chr19:56666517..56667150-chr19:56682928..56683556,2	MCF-7	breast:
7	chr19:56587463..56588432-chr19:56682914..56684123,6	K562	blood:
8	chr19:56591073..56592693-chr19:56682992..56683859,5	MCF-7	breast:
9	chr19:56577555..56578345-chr19:56683409..56683940,2	K562	blood:
10	chr19:56591703..56592615-chr19:56682968..56683865,3	K562	blood:

Variant related genes	Relation type
GALP	TF binding region
ENSG00000223060	Chromatin interaction
ENSG00000197487	Chromatin interaction
ENSG00000267522	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs16987029	0.89[JPT][hapmap]
rs16987031	0.89[JPT][hapmap]
rs2631642	0.84[EUR][1000 genomes]
rs2631652	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs274141	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274144	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs274145	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs274146	0.85[EUR][1000 genomes]
rs274151	0.84[EUR][1000 genomes]
rs274154	0.89[CEU][hapmap];0.84[CHB][hapmap];0.84[EUR][1000 genomes]
rs274155	0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs274159	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs274163	1.00[CEU][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs274165	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs274167	0.93[EUR][1000 genomes]
rs274168	0.89[CEU][hapmap];0.94[JPT][hapmap]
rs274182	0.89[CEU][hapmap]
rs3103059	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3103060	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs480528	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs481291	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs482506	0.82[ASN][1000 genomes]
rs487922	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs488118	0.82[ASN][1000 genomes]
rs488196	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs565171	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs581486	0.89[CEU][hapmap];0.85[CHB][hapmap];0.84[EUR][1000 genomes]
rs61283021	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs650832	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs651800	0.82[ASN][1000 genomes]
rs652204	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs671061	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs672956	0.90[ASN][1000 genomes]
rs679082	0.84[EUR][1000 genomes]
rs901476	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
11	nsv528361	chr19:56638845-56688570	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56672600-56684200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr19:56672600-56685600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:56673000-56690000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:56682000-56686400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:56682000-56687000	Weak transcription	Spleen	Spleen
6	chr19:56682200-56683600	Enhancers	HepG2	liver
7	chr19:56682200-56685400	Weak transcription	K562	blood
8	chr19:56682400-56683600	Weak transcription	Colonic Mucosa	Colon
9	chr19:56683200-56683600	Enhancers	Primary B cells from peripheral blood	blood
10	chr19:56683200-56683600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr19:56683200-56683600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr19:56683200-56683600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:56683200-56683600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr19:56683200-56683600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:56683200-56683600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:56683200-56683600	Enhancers	Liver	Liver
17	chr19:56683200-56683600	Enhancers	Brain Substantia Nigra	brain
18	chr19:56683200-56683600	Enhancers	Dnd41	blood
19	chr19:56683200-56683600	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr19:56683200-56683800	Enhancers	Primary hematopoietic stem cells	blood
21	chr19:56683200-56683800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr19:56683200-56684000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:56683400-56683600	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr19:56683400-56683600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:56683400-56683600	Enhancers	Fetal Intestine Large	intestine

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