Variant report

Variant	rs509897
Chromosome Location	chr19:56619664-56619665
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF143	chr19:56619510-56619870	H1-hESC	embryonic stem cell:	n/a	n/a
2	EGR1	chr19:56619445-56619919	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:56619342-56619810	HepG2	liver:	n/a	n/a
4	SIN3A	chr19:56619536-56619862	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:56619153-56619717	K562	blood:	n/a	n/a
6	POLR2A	chr19:56617422-56620971	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:56618269..56620601-chr19:56650918..56652939,2	MCF-7	breast:
2	chr19:56617972..56620643-chr19:56620884..56623590,3	MCF-7	breast:
3	chr19:56617470..56621508-chr19:56630958..56634094,7	MCF-7	breast:
4	chr19:56619067..56621819-chr19:56683473..56686134,2	K562	blood:
5	chr19:56618895..56620681-chr19:56648201..56650740,2	K562	blood:

No data

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

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11673628	0.81[ASN][1000 genomes]
rs12459102	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2450439	0.84[ASN][1000 genomes]
rs2631625	0.83[ASN][1000 genomes]
rs2631627	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2631628	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2631631	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2631637	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2631640	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2637092	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2637094	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2637097	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2637114	0.82[ASN][1000 genomes]
rs2932757	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35766803	0.83[ASN][1000 genomes]
rs473953	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs478402	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs481936	0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs490345	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs492078	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs497453	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs501798	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs504350	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs506547	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs517021	0.81[AMR][1000 genomes]
rs517582	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs521092	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs522980	0.87[AMR][1000 genomes]
rs524778	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs524829	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs524988	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs525827	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs527715	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs533640	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs533734	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs535393	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs536342	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs536414	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs537425	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs540900	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs547945	0.85[AMR][1000 genomes]
rs564050	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs564973	0.81[ASN][1000 genomes]
rs569310	0.82[ASN][1000 genomes]
rs570210	0.86[ASN][1000 genomes]
rs572851	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs578990	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs578991	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs582271	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs583330	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs588574	0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs592827	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs599405	0.85[AMR][1000 genomes]
rs609736	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs609755	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs619934	0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs626821	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs629544	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs630704	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs640654	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs642776	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs643133	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs643174	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs648352	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs659424	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs662308	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs662763	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs665082	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs665846	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs665857	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs667438	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs667974	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs677127	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs677142	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs678540	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs684653	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs685117	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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
19	esv3529768	chr19:56619530-56619843	Genic enhancers ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
20	esv3529769	chr19:56619530-56619843	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
21	esv3432566	chr19:56619594-56619912	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 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	chr19:56593000-56631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:56602800-56620000	Weak transcription	NH-A	brain
5	chr19:56603200-56619800	Weak transcription	NHDF-Ad	bronchial
6	chr19:56605200-56619800	Weak transcription	HSMM	muscle
7	chr19:56605200-56620000	Weak transcription	Fetal Kidney	kidney
8	chr19:56613200-56620000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr19:56613600-56619800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr19:56615000-56620200	Weak transcription	Aorta	Aorta
11	chr19:56616000-56619800	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr19:56616000-56626600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr19:56616000-56627000	Enhancers	Liver	Liver
14	chr19:56616000-56627200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr19:56616200-56620800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr19:56616600-56620400	Enhancers	Brain Hippocampus Middle	brain
17	chr19:56617000-56620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:56617200-56619800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:56617200-56619800	Enhancers	Primary hematopoietic stem cells	blood
20	chr19:56617200-56619800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr19:56617200-56619800	Strong transcription	Fetal Intestine Small	intestine
22	chr19:56617200-56619800	Weak transcription	Fetal Lung	lung
23	chr19:56617200-56620000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:56617200-56620000	Weak transcription	Fetal Brain Female	brain
25	chr19:56617200-56620000	Weak transcription	HUVEC	blood vessel
26	chr19:56617200-56620400	Weak transcription	Primary T cells from cord blood	blood
27	chr19:56617200-56622000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr19:56617200-56622800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:56617200-56624400	Weak transcription	Hela-S3	cervix
30	chr19:56617200-56629200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:56617400-56620000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr19:56617400-56620800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:56617400-56620800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr19:56617400-56621000	Genic enhancers	Lung	lung
35	chr19:56617400-56622400	Weak transcription	Fetal Brain Male	brain
36	chr19:56617400-56623400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr19:56617600-56619800	Weak transcription	Colon Smooth Muscle	Colon
38	chr19:56617600-56620000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr19:56617800-56619800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:56617800-56619800	Weak transcription	Brain Angular Gyrus	brain
41	chr19:56617800-56620400	Genic enhancers	Pancreas	Pancrea
42	chr19:56618000-56619800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:56618000-56621000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr19:56618200-56620000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:56618200-56620200	Enhancers	Gastric	stomach
46	chr19:56618200-56621000	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr19:56618200-56624400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr19:56618400-56619800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:56618400-56619800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr19:56618400-56619800	Weak transcription	HMEC	breast

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