Variant report

Variant	rs541316510
Chromosome Location	chr19:39902654-39902655
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	CTCF	chr19:39902560-39902710	MCF-7	breast:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
6	BHLHE40	chr19:39902437-39903612	A549	lung:	n/a	chr19:39903490-39903506
7	NFIC	chr19:39902514-39903672	ECC-1	luminal epithelium:	n/a	n/a
8	JUND	chr19:39901656-39903704	A549	lung:	n/a	chr19:39903202-39903211
9	POLR2A	chr19:39896853-39907805	IMR90	lung:	n/a	n/a
10	CUX1	chr19:39902142-39903108	K562	blood:	n/a	n/a
11	RAD21	chr19:39902365-39902803	GM12878	blood:	n/a	chr19:39902614-39902628 chr19:39902619-39902628 chr19:39902610-39902629 chr19:39902618-39902631
12	TEAD4	chr19:39902464-39903224	MCF-7	breast:	n/a	n/a
13	RAD21	chr19:39902165-39903070	A549	lung:	n/a	chr19:39902614-39902628 chr19:39902619-39902628 chr19:39902610-39902629 chr19:39902956-39902969 chr19:39902618-39902631
14	POLR2A	chr19:39896847-39904491	U87	brain:	n/a	n/a
15	CTCF	chr19:39902540-39902690	GM12801	blood:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
16	RPC155	chr19:39902536-39903163	K562	blood:	n/a	n/a
17	REST	chr19:39902547-39903277	PFSK-1	brain:	n/a	chr19:39903228-39903246 chr19:39903231-39903244
18	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
19	POLR2A	chr19:39902568-39903652	HUVEC	blood vessel:	n/a	n/a
20	CHD2	chr19:39902491-39903710	K562	blood:	n/a	chr19:39903196-39903206 chr19:39903199-39903209
21	SIN3AK20	chr19:39896816-39903789	HCT-116	colon:	n/a	n/a
22	TEAD4	chr19:39902569-39903630	ECC-1	luminal epithelium:	n/a	n/a
23	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
24	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
25	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
26	MXI1	chr19:39901770-39903512	GM12878	blood:	n/a	chr19:39902945-39902954
27	CTCF	chr19:39902560-39902710	GM12868	blood:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
28	GATA1	chr19:39902247-39903750	PBDE	blood:	n/a	n/a
29	HNF4G	chr19:39902435-39903381	HepG2	liver:	n/a	n/a
30	STAT3	chr19:39902620-39903205	MCF10A-Er-Src	breast:	n/a	n/a
31	ARID3A	chr19:39902479-39903168	K562	blood:	n/a	n/a
32	CTCF	chr19:39902520-39902670	Hela-S3	cervix:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
33	POLR2A	chr19:39897307-39904232	GM12878	blood:	n/a	n/a
34	TEAD4	chr19:39902472-39903306	HepG2	liver:	n/a	n/a
35	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
36	ATF3	chr19:39902510-39903519	K562	blood:	n/a	chr19:39903503-39903513 chr19:39903505-39903519 chr19:39903506-39903517
37	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
38	POLR2A	chr19:39899961-39903639	GM12891	blood:	n/a	n/a
39	IRF4	chr19:39902440-39903153	GM12878	blood:	n/a	n/a
40	CTCF	chr19:39902511-39902749	A549	lung:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
41	USF2	chr19:39901719-39903150	GM12878	blood:	n/a	n/a
42	CTCF	chr19:39902540-39902690	AG10803	skin:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
43	CTCF	chr19:39902540-39902690	GM12875	blood:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
44	YY1	chr19:39902423-39903067	GM12892	blood:	n/a	chr19:39902909-39902920 chr19:39902958-39902972
45	ETS1	chr19:39902281-39903710	A549	lung:	n/a	chr19:39903196-39903207 chr19:39903247-39903260 chr19:39903243-39903254 chr19:39903199-39903210 chr19:39903217-39903232
46	POLR2A	chr19:39902543-39904405	GM15510	blood:	n/a	n/a
47	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
48	CTCF	chr19:39902520-39902670	WERI-Rb-1	eye:	n/a	chr19:39902617-39902630 chr19:39902612-39902630 chr19:39902607-39902628 chr19:39902614-39902627 chr19:39902618-39902627 chr19:39902614-39902627
49	POLR2A	chr19:39896827-39903535	HCT-116	colon:	n/a	n/a
50	USF1	chr19:39902447-39903357	A549	lung:	n/a	chr19:39902943-39902954

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	chr1:249200195..249200966-chr19:39902171..39902702,2	Hela-S3	cervix:
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	chr19:39794184..39795931-chr19:39900825..39902976,2	K562	blood:
11	chr19:39902436..39904048-chr19:39969524..39972192,2	K562	blood:
12	chr19:39835965..39836894-chr19:39901884..39902780,2	MCF-7	breast:
13	chr19:39818884..39821188-chr19:39900599..39903098,4	K562	blood:
14	chr19:38878332..38880933-chr19:39901486..39903519,2	K562	blood:
15	chr19:39887994..39889005-chr19:39901768..39903114,14	MCF-7	breast:
16	chr19:39811404..39814084-chr19:39901271..39903376,2	MCF-7	breast:
17	chr19:39902218..39902729-chr6:111136205..111136730,2	Hela-S3	cervix:
18	chr19:39901022..39904778-chr19:40029097..40032980,4	MCF-7	breast:
19	chr19:39901043..39903228-chr6:26197435..26199053,2	K562	blood:
20	chr19:39341057..39343314-chr19:39902630..39904241,2	MCF-7	breast:
21	chr19:39898615..39904728-chr19:40019936..40025504,8	K562	blood:
22	chr19:39902391..39904212-chr19:39959568..39962203,2	K562	blood:
23	chr15:101816022..101818660-chr19:39901471..39903497,2	K562	blood:
24	chr19:39887960..39888930-chr19:39901705..39903106,10	MCF-7	breast:
25	chr19:39901846..39902823-chr3:129033270..129033809,2	Hela-S3	cervix:
26	chr19:39831269..39834563-chr19:39900586..39904953,4	MCF-7	breast:
27	chr19:39784841..39787662-chr19:39900971..39903770,2	K562	blood:
28	chr19:39902534..39904778-chr19:40022453..40024067,3	MCF-7	breast:
29	chr19:39859164..39862677-chr19:39900156..39904174,3	MCF-7	breast:
30	chr19:39902516..39903447-chr8:96036765..96037730,2	Hela-S3	cervix:
31	chr11:59383155..59384014-chr19:39902416..39902968,2	Hela-S3	cervix:
32	chr19:39828912..39834348-chr19:39896525..39904623,14	K562	blood:

Variant related genes	Relation type
MIR4530	TF binding region
PLEKHG2	TF binding region
ENSG00000155111	Chromatin interaction
ENSG00000156170	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000182393	Chromatin interaction
ENSG00000268262	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000255139	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000185220	Chromatin interaction
ENSG00000131871	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000188766	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000110048	Chromatin interaction
ENSG00000179168	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000241983	Chromatin interaction
ENSG00000197562	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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	chr19:39900400-39902800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
9	chr19:39900400-39902800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:39900400-39902800	Flanking Active TSS	HMEC	breast
11	chr19:39900600-39902800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr19:39900800-39902800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr19:39900800-39902800	Flanking Active TSS	Liver	Liver
14	chr19:39900800-39903200	Weak transcription	Small Intestine	intestine
15	chr19:39901000-39902800	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr19:39901000-39902800	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr19:39901000-39902800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr19:39901000-39902800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr19:39901000-39903200	Weak transcription	Ovary	ovary
20	chr19:39901600-39902800	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr19:39901600-39904600	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr19:39902000-39902800	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr19:39902000-39902800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr19:39902000-39902800	Flanking Active TSS	Fetal Kidney	kidney
25	chr19:39902000-39902800	Flanking Active TSS	Fetal Lung	lung
26	chr19:39902000-39903600	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr19:39902200-39903000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:39902200-39903000	Weak transcription	Left Ventricle	heart
29	chr19:39902200-39903200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:39902200-39903200	Weak transcription	Lung	lung
31	chr19:39902200-39904400	Active TSS	Fetal Muscle Trunk	muscle
32	chr19:39902200-39904400	Active TSS	Thymus	Thymus
33	chr19:39902200-39904600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:39902200-39904600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:39902200-39905000	Active TSS	Psoas Muscle	Psoas
36	chr19:39902200-39905200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:39902200-39905600	Active TSS	Right Ventricle	heart
38	chr19:39902200-39905800	Active TSS	Esophagus	oesophagus
39	chr19:39902400-39902800	Flanking Active TSS	Fetal Brain Male	brain
40	chr19:39902400-39902800	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr19:39902400-39902800	Flanking Active TSS	HUVEC	blood vessel
42	chr19:39902400-39903000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:39902400-39903000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr19:39902400-39903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:39902400-39903200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:39902400-39903200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:39902400-39903200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:39902400-39903200	Active TSS	Colonic Mucosa	Colon
49	chr19:39902400-39903200	Weak transcription	Pancreas	Pancrea
50	chr19:39902400-39903200	Weak transcription	Spleen	Spleen

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