Variant report

Variant	rs577252233
Chromosome Location	chr19:39901942-39901943
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	chr19:39898986-39905074	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3AK20	chr19:39895490-39907815	PANC-1	pancreas:	n/a	n/a
3	JUND	chr19:39901656-39903704	A549	lung:	n/a	chr19:39903202-39903211
4	POLR2A	chr19:39896853-39907805	IMR90	lung:	n/a	n/a
5	POLR2A	chr19:39896847-39904491	U87	brain:	n/a	n/a
6	MAFF	chr19:39901633-39902151	HepG2	liver:	n/a	n/a
7	SP1	chr19:39899875-39905378	A549	lung:	n/a	chr19:39904171-39904181 chr19:39904280-39904293 chr19:39904081-39904095 chr19:39903194-39903206 chr19:39903150-39903160 chr19:39904090-39904102 chr19:39900086-39900100 chr19:39904090-39904102 chr19:39904085-39904094 chr19:39903195-39903204 chr19:39904084-39904096 chr19:39904084-39904096 chr19:39903196-39903205 chr19:39903195-39903205 chr19:39903194-39903206 chr19:39903245-39903254 chr19:39902964-39902975 chr19:39904057-39904071 chr19:39903195-39903209 chr19:39904384-39904398 chr19:39903149-39903161
8	SIN3AK20	chr19:39896816-39903789	HCT-116	colon:	n/a	n/a
9	SMC3	chr19:39901471-39905350	SK-N-SH	brain:	n/a	chr19:39902614-39902624 chr19:39902621-39902628 chr19:39904476-39904486 chr19:39903477-39903491 chr19:39903480-39903490 chr19:39902614-39902628
10	TAF1	chr19:39901830-39902286	K562	blood:	n/a	n/a
11	MAX	chr19:39901732-39903677	GM12878	blood:	n/a	chr19:39902942-39902955 chr19:39903201-39903211 chr19:39902944-39902953 chr19:39902944-39902953 chr19:39902942-39902955 chr19:39902942-39902955 chr19:39903336-39903345 chr19:39903271-39903281 chr19:39902943-39902954
12	POLR2A	chr19:39899962-39902342	HL-60	blood:	n/a	n/a
13	MXI1	chr19:39901770-39903512	GM12878	blood:	n/a	chr19:39902945-39902954
14	SIN3AK20	chr19:39901702-39902088	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:39897307-39904232	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:39899961-39903639	GM12891	blood:	n/a	n/a
17	EP300	chr19:39901659-39902288	HepG2	liver:	n/a	n/a
18	USF2	chr19:39901719-39903150	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:39896827-39903535	HCT-116	colon:	n/a	n/a
20	SREBP2	chr19:39901296-39904141	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:39896460-39903920	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr19:39901493-39903435	HepG2	liver:	n/a	n/a
23	TBP	chr19:39901756-39903668	HepG2	liver:	n/a	n/a
24	JUND	chr19:39897180-39903728	HCT-116	colon:	n/a	chr19:39903202-39903211 chr19:39900169-39900178
25	CBX3	chr19:39901288-39903612	K562	blood:	n/a	n/a
26	NFIC	chr19:39901703-39903777	GM12878	blood:	n/a	n/a
27	HNF4A	chr19:39901644-39902104	HepG2	liver:	n/a	chr19:39901912-39901927
28	TCF12	chr19:39901508-39904131	A549	lung:	n/a	chr19:39902568-39902577 chr19:39903975-39903982
29	BRCA1	chr19:39901792-39902041	GM12878	blood:	n/a	n/a
30	HEY1	chr19:39901403-39903676	HepG2	liver:	n/a	chr19:39903234-39903249
31	POLR2A	chr19:39901637-39902198	HepG2	liver:	n/a	n/a
32	POLR2A	chr19:39897208-39903534	K562	blood:	n/a	n/a
33	MBD4	chr19:39901539-39903174	HepG2	liver:	n/a	n/a
34	YY1	chr19:39901661-39902054	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:39901352-39903007	HepG2	liver:	n/a	n/a
36	TAF1	chr19:39901766-39902154	HepG2	liver:	n/a	n/a
37	POLR2A	chr19:39901656-39902225	A549	lung:	n/a	n/a
38	USF1	chr19:39901493-39903881	A549	lung:	n/a	chr19:39903490-39903506 chr19:39902943-39902954
39	YY1	chr19:39901536-39902186	K562	blood:	n/a	n/a
40	POLR2A	chr19:39896847-39904730	U87	brain:	n/a	n/a
41	CHD1	chr19:39901644-39902079	GM12878	blood:	n/a	n/a
42	POU2F2	chr19:39901464-39902320	GM12878	blood:	n/a	n/a
43	MAX	chr19:39899953-39905593	A549	lung:	n/a	chr19:39902942-39902955 chr19:39903201-39903211 chr19:39900090-39900100 chr19:39902944-39902953 chr19:39902944-39902953 chr19:39902942-39902955 chr19:39902942-39902955 chr19:39903336-39903345 chr19:39903271-39903281 chr19:39904354-39904364 chr19:39904055-39904065 chr19:39904327-39904337 chr19:39904845-39904855 chr19:39902943-39902954
44	ZNF263	chr19:39900102-39903115	HEK293-T-REx	kidney:	n/a	chr19:39900926-39900947
45	SP1	chr19:39901668-39902287	HepG2	liver:	n/a	n/a
46	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr19:39899962-39903772	Hela-S3	cervix:	n/a	n/a
48	REST	chr19:39899959-39907266	PANC-1	pancreas:	n/a	chr19:39903228-39903246 chr19:39906163-39906176 chr19:39906087-39906100 chr19:39903231-39903244 chr19:39903569-39903583 chr19:39904389-39904402
49	JUND	chr19:39901628-39902321	A549	lung:	n/a	n/a
50	POU2F2	chr19:39901601-39902248	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39900130..39902222-chr19:40323529..40326104,2	MCF-7	breast:
2	chr19:39829936..39834375-chr19:39901478..39904741,5	MCF-7	breast:
3	chr19:39901242..39902227-chr2:109149697..109150593,2	Hela-S3	cervix:
4	chr19:39845356..39848788-chr19:39900821..39905638,4	MCF-7	breast:
5	chr19:39898615..39903463-chr19:40021264..40024360,6	K562	blood:
6	chr19:39618807..39620742-chr19:39901218..39902940,2	MCF-7	breast:
7	chr16:638070..640244-chr19:39901312..39902865,2	MCF-7	breast:
8	chr19:39874290..39876646-chr19:39900932..39903382,2	MCF-7	breast:
9	chr19:39855401..39857094-chr19:39901000..39902939,2	MCF-7	breast:
10	chr14:35515332..35516104-chr19:39901371..39902212,2	Hela-S3	cervix:
11	chr19:39794184..39795931-chr19:39900825..39902976,2	K562	blood:
12	chr17:62502403..62503186-chr19:39901446..39901977,2	Hela-S3	cervix:
13	chr19:39835965..39836894-chr19:39901884..39902780,2	MCF-7	breast:
14	chr10:112261063..112261639-chr19:39901432..39902241,2	Hela-S3	cervix:
15	chr19:39901493..39902364-chr5:6712772..6713730,2	Hela-S3	cervix:
16	chr19:39818884..39821188-chr19:39900599..39903098,4	K562	blood:
17	chr19:39901637..39902610-chr3:9439074..9439778,2	Hela-S3	cervix:
18	chr19:38878332..38880933-chr19:39901486..39903519,2	K562	blood:
19	chr19:39900714..39902326-chr19:40314340..40316336,2	MCF-7	breast:
20	chr19:39887994..39889005-chr19:39901768..39903114,14	MCF-7	breast:
21	chr19:39811404..39814084-chr19:39901271..39903376,2	MCF-7	breast:
22	chr19:39901022..39904778-chr19:40029097..40032980,4	MCF-7	breast:
23	chr19:39901043..39903228-chr6:26197435..26199053,2	K562	blood:
24	chr19:39898615..39904728-chr19:40019936..40025504,8	K562	blood:
25	chr15:101816022..101818660-chr19:39901471..39903497,2	K562	blood:
26	chr19:39887960..39888930-chr19:39901705..39903106,10	MCF-7	breast:
27	chr19:39901637..39902618-chr19:40926654..40927443,2	Hela-S3	cervix:
28	chr19:39901846..39902823-chr3:129033270..129033809,2	Hela-S3	cervix:
29	chr19:39831269..39834563-chr19:39900586..39904953,4	MCF-7	breast:
30	chr19:39898553..39902206-chr19:39948362..39950815,3	K562	blood:
31	chr19:39784841..39787662-chr19:39900971..39903770,2	K562	blood:
32	chr19:39859164..39862677-chr19:39900156..39904174,3	MCF-7	breast:
33	chr19:39828912..39834348-chr19:39896525..39904623,14	K562	blood:

Variant related genes	Relation type
PLEKHG2	TF binding region
MIR4530	TF binding region
ENSG00000168137	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000182393	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000131871	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000105204	Chromatin interaction
ENSG00000241983	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000151327	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000197562	Chromatin interaction
ENSG00000268262	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
7	nsv911684	chr19:39886218-39923863	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
9	nsv911686	chr19:39891219-39907781	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
10	nsv911687	chr19:39891219-39909714	Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	171 gene(s)	inside rSNPs	diseases
11	nsv911688	chr19:39891219-39919538	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
12	esv1832456	chr19:39901611-39914748	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	45 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39899400-39902000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:39899400-39905200	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr19:39899400-39905800	Active TSS	Aorta	Aorta
4	chr19:39899600-39902800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:39899800-39903200	Weak transcription	Gastric	stomach
6	chr19:39900000-39902800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr19:39900000-39902800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:39900000-39902800	Flanking Active TSS	Dnd41	blood
9	chr19:39900200-39902600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr19:39900400-39902400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr19:39900400-39902600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:39900400-39902800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr19:39900400-39902800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:39900400-39902800	Flanking Active TSS	HMEC	breast
15	chr19:39900600-39902200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr19:39900600-39902400	Flanking Active TSS	Colonic Mucosa	Colon
17	chr19:39900600-39902400	Flanking Active TSS	GM12878-XiMat	blood
18	chr19:39900600-39902600	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr19:39900600-39902600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:39900600-39902600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr19:39900600-39902800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr19:39900800-39902200	Flanking Active TSS	HSMM	muscle
23	chr19:39900800-39902400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:39900800-39902400	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr19:39900800-39902400	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr19:39900800-39902400	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr19:39900800-39902600	Flanking Active TSS	Hela-S3	cervix
28	chr19:39900800-39902600	Flanking Active TSS	HSMMtube	muscle
29	chr19:39900800-39902800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr19:39900800-39902800	Flanking Active TSS	Liver	Liver
31	chr19:39900800-39903200	Weak transcription	Small Intestine	intestine
32	chr19:39901000-39902000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr19:39901000-39902200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr19:39901000-39902200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:39901000-39902200	Flanking Active TSS	Left Ventricle	heart
36	chr19:39901000-39902200	Flanking Active TSS	Right Ventricle	heart
37	chr19:39901000-39902400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:39901000-39902400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:39901000-39902400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:39901000-39902400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr19:39901000-39902400	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr19:39901000-39902400	Enhancers	Placenta Amnion	Placenta Amnion
43	chr19:39901000-39902400	Enhancers	Spleen	Spleen
44	chr19:39901000-39902400	Flanking Active TSS	NHDF-Ad	bronchial
45	chr19:39901000-39902400	Flanking Active TSS	Osteobl	bone
46	chr19:39901000-39902600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr19:39901000-39902600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr19:39901000-39902600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:39901000-39902600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:39901000-39902600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links