Variant report

Variant	rs578901
Chromosome Location	chr19:56615160-56615161
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	POLR2A	chr19:56614878-56616247	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:56615052-56615916	A549	lung:	n/a	n/a
3	TCF3	chr19:56615034-56615990	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:56615053-56616074	GM12878	blood:	n/a	n/a
5	TAF1	chr19:56615084-56615957	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:56615100-56616027	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:56615108-56616163	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:56615099-56616120	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:56615019-56615996	A549	lung:	n/a	n/a
10	POLR2A	chr19:56614957-56616149	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:56615054-56615991	A549	lung:	n/a	n/a
12	POLR2A	chr19:56614982-56616153	GM12891	blood:	n/a	n/a
13	POLR2A	chr19:56615131-56616113	GM12892	blood:	n/a	n/a
14	REST	chr19:56615091-56615977	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr19:56614965-56616076	GM12892	blood:	n/a	n/a
16	POLR2A	chr19:56614986-56616181	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56612599..56616950-chr19:56825214..56827593,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223060	TF binding region
ZNF787	TF binding region
ENSG00000131848	Chromatin interaction
ENSG00000267549	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2279413	0.82[EUR][1000 genomes]
rs494615	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs513915	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs514916	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs516022	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58893103	0.81[EUR][1000 genomes]
rs62122447	0.81[EUR][1000 genomes]
rs62122448	0.81[EUR][1000 genomes]
rs62122451	0.82[EUR][1000 genomes]
rs62122452	0.82[EUR][1000 genomes]
rs62122455	0.82[EUR][1000 genomes]
rs6509983	0.84[ASN][1000 genomes]
rs7253923	0.85[ASN][1000 genomes]
rs7254130	0.85[ASN][1000 genomes]
rs7254265	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	nsv912515	chr19:56598829-56623710	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
15	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
16	esv1809307	chr19:56604027-56633623	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
17	esv1811581	chr19:56609313-56631618	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
18	esv1824038	chr19:56610449-56636632	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56592600-56620000	Weak transcription	HSMMtube	muscle
2	chr19:56592800-56622600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr19:56593000-56616200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:56593000-56616600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:56593000-56616800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:56593600-56616000	Weak transcription	Stomach Mucosa	stomach
8	chr19:56594800-56616800	Weak transcription	HUVEC	blood vessel
9	chr19:56597200-56619400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:56599800-56615200	Strong transcription	Liver	Liver
11	chr19:56600000-56619000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:56600800-56616800	Weak transcription	Small Intestine	intestine
13	chr19:56602800-56620000	Weak transcription	NH-A	brain
14	chr19:56603000-56616600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:56603200-56619800	Weak transcription	NHDF-Ad	bronchial
16	chr19:56603800-56616800	Weak transcription	Psoas Muscle	Psoas
17	chr19:56604800-56616200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:56604800-56616800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:56605000-56616400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:56605200-56617000	Weak transcription	Brain Angular Gyrus	brain
21	chr19:56605200-56619800	Weak transcription	HSMM	muscle
22	chr19:56605200-56620000	Weak transcription	Fetal Kidney	kidney
23	chr19:56606000-56615800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr19:56606200-56615200	Strong transcription	Colonic Mucosa	Colon
25	chr19:56606200-56615200	Strong transcription	Thymus	Thymus
26	chr19:56606400-56615200	Strong transcription	Esophagus	oesophagus
27	chr19:56606400-56615200	Strong transcription	A549	lung
28	chr19:56606400-56616600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr19:56608000-56615200	Genic enhancers	Spleen	Spleen
30	chr19:56608200-56615200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:56608200-56618600	ZNF genes & repeats	Brain Germinal Matrix	brain
32	chr19:56609000-56616000	Weak transcription	Right Atrium	heart
33	chr19:56609600-56619600	Weak transcription	Fetal Heart	heart
34	chr19:56610200-56615200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr19:56610800-56616000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr19:56611200-56615400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr19:56611400-56617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:56611600-56616800	Strong transcription	Fetal Intestine Small	intestine
39	chr19:56611800-56615800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:56612400-56615200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:56612600-56616000	Strong transcription	Gastric	stomach
42	chr19:56612800-56615200	Strong transcription	NHEK	skin
43	chr19:56613000-56615200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr19:56613000-56615200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr19:56613000-56616000	Weak transcription	Colon Smooth Muscle	Colon
46	chr19:56613200-56616000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:56613200-56616800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:56613200-56620000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:56613400-56616800	Weak transcription	Osteobl	bone
50	chr19:56613600-56619800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

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