Variant report

Variant	rs3746085
Chromosome Location	chr19:39904756-39904757
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	CEBPB	chr19:39904444-39905542	A549	lung:	n/a	n/a
4	UBTF	chr19:39904724-39905103	K562	blood:	n/a	n/a
5	E2F6	chr19:39902021-39905287	A549	lung:	n/a	chr19:39903297-39903309 chr19:39904360-39904372 chr19:39903210-39903222 chr19:39904126-39904135
6	POLR2A	chr19:39896853-39907805	IMR90	lung:	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	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
9	POLR2A	chr19:39904375-39904806	GM12878	blood:	n/a	n/a
10	TAF1	chr19:39902747-39904976	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr19:39904729-39905028	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:39904645-39905071	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:39904652-39905095	A549	lung:	n/a	n/a
14	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
15	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
16	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
17	MAZ	chr19:39896170-39907106	IMR90	lung:	n/a	chr19:39902942-39902955 chr19:39903201-39903211 chr19:39906097-39906107 chr19:39900090-39900100 chr19:39897711-39897721 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
18	CTCF	chr19:39904737-39905106	K562	blood:	n/a	n/a
19	CTCF	chr19:39904747-39905194	A549	lung:	n/a	n/a
20	MTA3	chr19:39896751-39905454	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:39904681-39905083	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:39904563-39905652	Hela-S3	cervix:	n/a	n/a
23	SP1	chr19:39904138-39905348	A549	lung:	n/a	chr19:39904171-39904181 chr19:39904280-39904293 chr19:39904384-39904398
24	ELF1	chr19:39902753-39905151	GM12878	blood:	n/a	chr19:39903317-39903326 chr19:39904848-39904860
25	POLR2A	chr19:39904598-39905161	A549	lung:	n/a	n/a
26	PML	chr19:39901568-39904825	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:39897140-39907785	H1-hESC	embryonic stem cell:	n/a	n/a
28	ZEB1	chr19:39904578-39905016	GM12878	blood:	n/a	chr19:39904832-39904841
29	POLR2A	chr19:39902456-39905170	HUVEC	blood vessel:	n/a	n/a
30	JUND	chr19:39903842-39905236	A549	lung:	n/a	n/a
31	YY1	chr19:39902384-39905141	A549	lung:	n/a	chr19:39904851-39904862 chr19:39904382-39904393 chr19:39903826-39903834 chr19:39904088-39904102 chr19:39903317-39903326 chr19:39902909-39902920 chr19:39904091-39904100 chr19:39904353-39904362 chr19:39904058-39904069 chr19:39904184-39904195 chr19:39902958-39902972
32	REST	chr19:39902181-39905421	H1-neurons	neurons:	n/a	chr19:39903228-39903246 chr19:39903231-39903244 chr19:39903569-39903583 chr19:39904389-39904402
33	POLR2A	chr19:39904637-39905033	H1-hESC	embryonic stem cell:	n/a	n/a
34	TCF12	chr19:39896099-39906168	A549	lung:	n/a	chr19:39902568-39902577 chr19:39903975-39903982
35	FOSL2	chr19:39898972-39905550	A549	lung:	n/a	chr19:39903202-39903211 chr19:39900169-39900178
36	CTCF	chr19:39904720-39904870	GM12865	blood:	n/a	n/a
37	POLR2A	chr19:39904593-39904865	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:39896687-39907801	GM12878	blood:	n/a	n/a
39	HMGN3	chr19:39904400-39904878	K562	blood:	n/a	n/a
40	ZBTB7A	chr19:39902870-39904767	ECC-1	luminal epithelium:	n/a	chr19:39903476-39903485
41	POLR2A	chr19:39902431-39905188	H1-neurons	neurons:	n/a	n/a
42	POLR2A	chr19:39903957-39904762	ProgFib	skin:	n/a	n/a
43	EP300	chr19:39904198-39905333	A549	lung:	n/a	n/a
44	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr19:39904744-39905181	PFSK-1	brain:	n/a	n/a
46	POLR2A	chr19:39904586-39906838	GM12892	blood:	n/a	n/a
47	REST	chr19:39898501-39905504	A549	lung:	n/a	chr19:39903228-39903246 chr19:39903231-39903244 chr19:39903569-39903583 chr19:39904389-39904402
48	POLR2A	chr19:39896760-39904986	Hela-S3	cervix:	n/a	n/a
49	SIN3AK20	chr19:39904122-39904792	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr19:39902482-39905325	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39845356..39848788-chr19:39900821..39905638,4	MCF-7	breast:
2	chr19:39903969..39906470-chr19:39964577..39967105,2	MCF-7	breast:
3	chr19:39903148..39905900-chr19:39965149..39967658,2	K562	blood:
4	chr19:39901022..39904778-chr19:40029097..40032980,4	MCF-7	breast:
5	chr19:39831269..39834563-chr19:39900586..39904953,4	MCF-7	breast:
6	chr19:38753937..38756073-chr19:39903139..39906135,2	MCF-7	breast:
7	chr19:39903188..39905724-chr19:39934407..39937965,7	MCF-7	breast:
8	chr19:39902534..39904778-chr19:40022453..40024067,3	MCF-7	breast:

Variant related genes	Relation type
MIR4530	TF binding region
PLEKHG2	TF binding region
ENSG00000179134	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000196235	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11672196	1.00[MEX][hapmap]
rs12980978	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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
12	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
13	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 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	chr19:39899400-39905200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr19:39899400-39905800	Active TSS	Aorta	Aorta
3	chr19:39902200-39905000	Active TSS	Psoas Muscle	Psoas
4	chr19:39902200-39905200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:39902200-39905600	Active TSS	Right Ventricle	heart
6	chr19:39902200-39905800	Active TSS	Esophagus	oesophagus
7	chr19:39902400-39904800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr19:39902400-39904800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:39902400-39904800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:39902400-39904800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:39902400-39904800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:39902400-39904800	Active TSS	GM12878-XiMat	blood
13	chr19:39902400-39904800	Active TSS	Osteobl	bone
14	chr19:39902400-39905000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr19:39902400-39905000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:39902400-39905000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:39902400-39905000	Active TSS	NHLF	lung
18	chr19:39902400-39905200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr19:39902400-39905200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:39902400-39905200	Active TSS	Brain Hippocampus Middle	brain
21	chr19:39902400-39905600	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr19:39902400-39906000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr19:39902600-39904800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr19:39902600-39904800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:39902600-39904800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:39902600-39904800	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr19:39902600-39905000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:39902600-39905000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:39902600-39905000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr19:39902600-39905000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr19:39902600-39905000	Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr19:39902600-39905000	Active TSS	Brain Angular Gyrus	brain
33	chr19:39902600-39905000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:39902600-39905000	Active TSS	Fetal Brain Female	brain
35	chr19:39902600-39905000	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr19:39902600-39905000	Active TSS	NH-A	brain
37	chr19:39902600-39905200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr19:39902600-39905200	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr19:39902600-39905200	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr19:39902600-39905200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr19:39902600-39905200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:39902600-39905200	Active TSS	HSMM	muscle
43	chr19:39902600-39905600	Active TSS	Brain Cingulate Gyrus	brain
44	chr19:39902600-39905800	Active TSS	Brain Anterior Caudate	brain
45	chr19:39902800-39904800	Active TSS	Fetal Lung	lung
46	chr19:39902800-39904800	Active TSS	Fetal Stomach	stomach
47	chr19:39902800-39905200	Active TSS	Fetal Kidney	kidney
48	chr19:39903000-39904800	Active TSS	Placenta Amnion	Placenta Amnion
49	chr19:39903000-39905800	Active TSS	Left Ventricle	heart
50	chr19:39903200-39904800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

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