Variant report

Variant	rs556479169
Chromosome Location	chr19:39902455-39902456
allele	A/G
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	POLR2A	chr19:39902416-39903069	HCT-116	colon:	n/a	n/a
3	SIN3AK20	chr19:39895490-39907815	PANC-1	pancreas:	n/a	n/a
4	E2F6	chr19:39902021-39905287	A549	lung:	n/a	chr19:39903297-39903309 chr19:39904360-39904372 chr19:39903210-39903222 chr19:39904126-39904135
5	BHLHE40	chr19:39902437-39903612	A549	lung:	n/a	chr19:39903490-39903506
6	JUND	chr19:39901656-39903704	A549	lung:	n/a	chr19:39903202-39903211
7	POLR2A	chr19:39896853-39907805	IMR90	lung:	n/a	n/a
8	CUX1	chr19:39902142-39903108	K562	blood:	n/a	n/a
9	RAD21	chr19:39902365-39902803	GM12878	blood:	n/a	chr19:39902614-39902628 chr19:39902619-39902628 chr19:39902610-39902629 chr19:39902618-39902631
10	RAD21	chr19:39902165-39903070	A549	lung:	n/a	chr19:39902614-39902628 chr19:39902619-39902628 chr19:39902610-39902629 chr19:39902956-39902969 chr19:39902618-39902631
11	POLR2A	chr19:39896847-39904491	U87	brain:	n/a	n/a
12	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
13	SIN3AK20	chr19:39896816-39903789	HCT-116	colon:	n/a	n/a
14	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
15	CTCF	chr19:39902454-39902779	K562	blood:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
16	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
17	MXI1	chr19:39901770-39903512	GM12878	blood:	n/a	chr19:39902945-39902954
18	GATA1	chr19:39902247-39903750	PBDE	blood:	n/a	n/a
19	HNF4G	chr19:39902435-39903381	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:39897307-39904232	GM12878	blood:	n/a	n/a
21	MAZ	chr19:39902431-39903694	K562	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
22	CTCF	chr19:39902362-39902823	HepG2	liver:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
23	POLR2A	chr19:39899961-39903639	GM12891	blood:	n/a	n/a
24	IRF4	chr19:39902440-39903153	GM12878	blood:	n/a	n/a
25	USF2	chr19:39901719-39903150	GM12878	blood:	n/a	n/a
26	YY1	chr19:39902423-39903067	GM12892	blood:	n/a	chr19:39902909-39902920 chr19:39902958-39902972
27	ETS1	chr19:39902281-39903710	A549	lung:	n/a	chr19:39903196-39903207 chr19:39903247-39903260 chr19:39903243-39903254 chr19:39903199-39903210 chr19:39903217-39903232
28	CTCF	chr19:39902372-39903725	GM12878	blood:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39903477-39903490 chr19:39902614-39902627 chr19:39903476-39903492 chr19:39902618-39902627 chr19:39902614-39902627 chr19:39903006-39903024 chr19:39903475-39903493
29	POLR2A	chr19:39896827-39903535	HCT-116	colon:	n/a	n/a
30	USF1	chr19:39902447-39903357	A549	lung:	n/a	chr19:39902943-39902954
31	RAD21	chr19:39902275-39903612	Hela-S3	cervix:	n/a	chr19:39902614-39902628 chr19:39903473-39903492 chr19:39902619-39902628 chr19:39902610-39902629 chr19:39902956-39902969 chr19:39902618-39902631
32	SREBP2	chr19:39901296-39904141	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:39896460-39903920	MCF10A-Er-Src	breast:	n/a	n/a
34	TBP	chr19:39902404-39903646	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr19:39901493-39903435	HepG2	liver:	n/a	n/a
36	KAP1	chr19:39901982-39903417	U2OS	brain:	n/a	n/a
37	TBP	chr19:39901756-39903668	HepG2	liver:	n/a	n/a
38	JUND	chr19:39897180-39903728	HCT-116	colon:	n/a	chr19:39903202-39903211 chr19:39900169-39900178
39	CBX3	chr19:39901288-39903612	K562	blood:	n/a	n/a
40	NFIC	chr19:39901703-39903777	GM12878	blood:	n/a	n/a
41	TCF12	chr19:39901508-39904131	A549	lung:	n/a	chr19:39902568-39902577 chr19:39903975-39903982
42	MAX	chr19:39902419-39903719	SK-N-SH	brain:	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
43	HEY1	chr19:39901403-39903676	HepG2	liver:	n/a	chr19:39903234-39903249
44	STAT1	chr19:39902446-39903632	GM12878	blood:	n/a	chr19:39903197-39903209 chr19:39903196-39903208
45	CTCF	chr19:39902438-39902781	HepG2	liver:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
46	TBL1XR1	chr19:39902438-39903606	GM12878	blood:	n/a	n/a
47	POLR2A	chr19:39897208-39903534	K562	blood:	n/a	n/a
48	MBD4	chr19:39901539-39903174	HepG2	liver:	n/a	n/a
49	RAD21	chr19:39902188-39903778	ECC-1	luminal epithelium:	n/a	chr19:39902614-39902628 chr19:39903473-39903492 chr19:39902619-39902628 chr19:39902610-39902629 chr19:39902956-39902969 chr19:39902618-39902631
50	SP1	chr19:39902401-39903372	HepG2	liver:	n/a	chr19:39903194-39903206 chr19:39903150-39903160 chr19:39903195-39903204 chr19:39903196-39903205 chr19:39903195-39903205 chr19:39903194-39903206 chr19:39903245-39903254 chr19:39902964-39902975 chr19:39903195-39903209 chr19:39903149-39903161

No.	Distal block	Cell Line	Cell type
1	chr19:39829936..39834375-chr19:39901478..39904741,5	MCF-7	breast:
2	chr16:87351191..87351907-chr19:39901971..39902952,2	Hela-S3	cervix:
3	chr19:39845356..39848788-chr19:39900821..39905638,4	MCF-7	breast:
4	chr14:50358974..50359752-chr19:39902002..39902600,2	Hela-S3	cervix:
5	chr1:249200195..249200966-chr19:39902171..39902702,2	Hela-S3	cervix:
6	chr19:39898615..39903463-chr19:40021264..40024360,6	K562	blood:
7	chr19:39618807..39620742-chr19:39901218..39902940,2	MCF-7	breast:
8	chr16:638070..640244-chr19:39901312..39902865,2	MCF-7	breast:
9	chr19:39874290..39876646-chr19:39900932..39903382,2	MCF-7	breast:
10	chr19:39855401..39857094-chr19:39901000..39902939,2	MCF-7	breast:
11	chr19:39794184..39795931-chr19:39900825..39902976,2	K562	blood:
12	chr19:39902436..39904048-chr19:39969524..39972192,2	K562	blood:
13	chr19:39835965..39836894-chr19:39901884..39902780,2	MCF-7	breast:
14	chr19:39818884..39821188-chr19:39900599..39903098,4	K562	blood:
15	chr19:39901637..39902610-chr3:9439074..9439778,2	Hela-S3	cervix:
16	chr19:38878332..38880933-chr19:39901486..39903519,2	K562	blood:
17	chr19:39887994..39889005-chr19:39901768..39903114,14	MCF-7	breast:
18	chr19:39811404..39814084-chr19:39901271..39903376,2	MCF-7	breast:
19	chr19:39902218..39902729-chr6:111136205..111136730,2	Hela-S3	cervix:
20	chr19:39901022..39904778-chr19:40029097..40032980,4	MCF-7	breast:
21	chr19:39901043..39903228-chr6:26197435..26199053,2	K562	blood:
22	chr19:39898615..39904728-chr19:40019936..40025504,8	K562	blood:
23	chr19:39902391..39904212-chr19:39959568..39962203,2	K562	blood:
24	chr15:101816022..101818660-chr19:39901471..39903497,2	K562	blood:
25	chr19:39887960..39888930-chr19:39901705..39903106,10	MCF-7	breast:
26	chr19:39901637..39902618-chr19:40926654..40927443,2	Hela-S3	cervix:
27	chr19:39901846..39902823-chr3:129033270..129033809,2	Hela-S3	cervix:
28	chr19:39831269..39834563-chr19:39900586..39904953,4	MCF-7	breast:
29	chr19:39784841..39787662-chr19:39900971..39903770,2	K562	blood:
30	chr19:39859164..39862677-chr19:39900156..39904174,3	MCF-7	breast:
31	chr11:59383155..59384014-chr19:39902416..39902968,2	Hela-S3	cervix:
32	chr19:39902002..39902625-chr9:135819461..135819993,2	Hela-S3	cervix:
33	chr19:39828912..39834348-chr19:39896525..39904623,14	K562	blood:

Variant related genes	Relation type
MIR4530	TF binding region
PLEKHG2	TF binding region
ENSG00000197562	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000255139	Chromatin interaction
ENSG00000110048	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000165699	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000241983	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000268262	Chromatin interaction
ENSG00000131871	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000185220	Chromatin interaction
ENSG00000155111	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000182393	Chromatin interaction
ENSG00000168137	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39899400-39905200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr19:39899400-39905800	Active TSS	Aorta	Aorta
3	chr19:39899600-39902800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:39899800-39903200	Weak transcription	Gastric	stomach
5	chr19:39900000-39902800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr19:39900000-39902800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:39900000-39902800	Flanking Active TSS	Dnd41	blood
8	chr19:39900200-39902600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr19:39900400-39902600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:39900400-39902800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr19:39900400-39902800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:39900400-39902800	Flanking Active TSS	HMEC	breast
13	chr19:39900600-39902600	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr19:39900600-39902600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr19:39900600-39902600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr19:39900600-39902800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr19:39900800-39902600	Flanking Active TSS	Hela-S3	cervix
18	chr19:39900800-39902600	Flanking Active TSS	HSMMtube	muscle
19	chr19:39900800-39902800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr19:39900800-39902800	Flanking Active TSS	Liver	Liver
21	chr19:39900800-39903200	Weak transcription	Small Intestine	intestine
22	chr19:39901000-39902600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:39901000-39902600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr19:39901000-39902600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:39901000-39902600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:39901000-39902600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
27	chr19:39901000-39902600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr19:39901000-39902600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr19:39901000-39902600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:39901000-39902600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr19:39901000-39902600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:39901000-39902600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr19:39901000-39902600	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr19:39901000-39902600	Flanking Active TSS	Fetal Intestine Large	intestine
35	chr19:39901000-39902600	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr19:39901000-39902600	Flanking Active TSS	A549	lung
37	chr19:39901000-39902800	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr19:39901000-39902800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr19:39901000-39902800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr19:39901000-39902800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr19:39901000-39903200	Weak transcription	Ovary	ovary
42	chr19:39901200-39902600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr19:39901200-39902600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr19:39901200-39902600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr19:39901200-39902600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:39901200-39902600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr19:39901200-39902600	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr19:39901200-39902600	Enhancers	Placenta	Placenta
49	chr19:39901200-39902600	Flanking Active TSS	HepG2	liver
50	chr19:39901400-39902600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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