Variant report

Variant	rs672824
Chromosome Location	chr19:56636759-56636760
allele	A/C
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	USF2	chr19:56636736-56636890	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56636040..56638265-chr19:56651210..56653201,2	K562	blood:
2	chr19:56635952..56638231-chr19:56646331..56649019,3	MCF-7	breast:
3	chr19:56634814..56637617-chr19:56650729..56653163,3	MCF-7	breast:
4	chr19:56630485..56634048-chr19:56635782..56640573,5	MCF-7	breast:

Variant related genes	Relation type
ZNF787	TF binding region
ENSG00000142409	Chromatin interaction
ENSG00000167685	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10409172	1.00[JPT][hapmap];0.80[YRI][hapmap]
rs11673628	0.89[CEU][hapmap]
rs12983086	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap]
rs2631626	0.81[ASN][1000 genomes]
rs28553904	1.00[JPT][hapmap]
rs473045	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4801676	0.80[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap]
rs499083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs506986	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs529291	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs546082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs562907	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs8103672	0.87[GIH][hapmap];1.00[TSI][hapmap]
rs9676765	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv912512	chr19:56592286-56636759	Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
10	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv912514	chr19:56596815-56636759	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
14	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56633400-56636800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:56633400-56636800	Weak transcription	HSMM	muscle
3	chr19:56633400-56637000	Weak transcription	Left Ventricle	heart
4	chr19:56633600-56636800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr19:56633600-56636800	Weak transcription	Colonic Mucosa	Colon
6	chr19:56633600-56636800	Weak transcription	Placenta	Placenta
7	chr19:56633600-56636800	Weak transcription	Pancreas	Pancrea
8	chr19:56633600-56636800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:56633600-56636800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr19:56633600-56636800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr19:56633600-56636800	Weak transcription	HSMMtube	muscle
12	chr19:56633600-56637000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:56633600-56637000	Weak transcription	Psoas Muscle	Psoas
14	chr19:56633600-56637000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr19:56633600-56637200	Weak transcription	Fetal Intestine Small	intestine
16	chr19:56633600-56637400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:56633600-56637400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr19:56633600-56637400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr19:56633600-56637400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr19:56633600-56637400	Weak transcription	Fetal Intestine Large	intestine
21	chr19:56633600-56637600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr19:56633600-56638400	Weak transcription	Spleen	Spleen
23	chr19:56633600-56638800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr19:56633600-56639400	Enhancers	Primary T cells from cord blood	blood
25	chr19:56633800-56637000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:56633800-56637200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr19:56633800-56637400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr19:56633800-56637800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr19:56633800-56637800	Weak transcription	Fetal Kidney	kidney
30	chr19:56634000-56637400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:56634000-56640800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:56634000-56645400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr19:56634400-56638400	Enhancers	Fetal Thymus	thymus
34	chr19:56634800-56636800	Weak transcription	Fetal Stomach	stomach
35	chr19:56634800-56637400	Enhancers	Thymus	Thymus
36	chr19:56635000-56636800	Weak transcription	Fetal Lung	lung
37	chr19:56636200-56636800	Enhancers	HepG2	liver
38	chr19:56636200-56639200	Enhancers	Fetal Muscle Trunk	muscle
39	chr19:56636200-56639200	Enhancers	Fetal Muscle Leg	muscle
40	chr19:56636400-56637200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr19:56636600-56637000	Enhancers	K562	blood

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