Variant report

Variant	rs6509940
Chromosome Location	chr19:55883879-55883880
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	EP300	chr19:55883393-55886386	A549	lung:	n/a	chr19:55885754-55885770 chr19:55886005-55886012
2	SP1	chr19:55883338-55886333	A549	lung:	n/a	chr19:55885846-55885860 chr19:55885852-55885864 chr19:55885853-55885867 chr19:55885846-55885856 chr19:55883767-55883779 chr19:55885853-55885863 chr19:55883838-55883852 chr19:55883764-55883778 chr19:55885846-55885855 chr19:55885845-55885857 chr19:55885846-55885856 chr19:55885847-55885856 chr19:55885852-55885864 chr19:55883768-55883777 chr19:55885846-55885855 chr19:55885845-55885857 chr19:55885854-55885863
3	JUND	chr19:55883601-55886334	A549	lung:	n/a	chr19:55884279-55884289 chr19:55884362-55884372 chr19:55885416-55885425 chr19:55884363-55884371 chr19:55884362-55884372 chr19:55885848-55885857
4	BCL3	chr19:55883861-55884932	A549	lung:	n/a	chr19:55884199-55884208
5	NR2F2	chr19:55883863-55884636	MCF-7	breast:	n/a	n/a
6	ZBTB7A	chr19:55883652-55884460	K562	blood:	n/a	chr19:55884187-55884195
7	POLR2A	chr19:55883488-55883973	Hela-S3	cervix:	n/a	n/a
8	PBX3	chr19:55883291-55884712	A549	lung:	n/a	n/a
9	POLR2A	chr19:55883178-55886272	IMR90	lung:	n/a	n/a
10	CHD2	chr19:55883635-55884509	Hela-S3	cervix:	n/a	chr19:55883767-55883777
11	MAZ	chr19:55883230-55886457	IMR90	lung:	n/a	n/a
12	POLR2A	chr19:55883812-55883980	A549	lung:	n/a	n/a
13	POLR2A	chr19:55883638-55884412	MCF-7	breast:	n/a	n/a
14	REST	chr19:55883778-55884505	A549	lung:	n/a	n/a
15	MAX	chr19:55883811-55884577	A549	lung:	n/a	n/a
16	POLR2A	chr19:55883613-55884421	A549	lung:	n/a	n/a
17	FOSL2	chr19:55883380-55884643	A549	lung:	n/a	chr19:55884279-55884289 chr19:55884362-55884372 chr19:55884277-55884288 chr19:55884363-55884371 chr19:55884362-55884372
18	YY1	chr19:55883847-55884422	A549	lung:	n/a	n/a
19	MAX	chr19:55883227-55884650	A549	lung:	n/a	n/a
20	TFAP2C	chr19:55883403-55884560	Hela-S3	cervix:	n/a	chr19:55884414-55884429 chr19:55884391-55884406
21	POLR2A	chr19:55883254-55886288	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr19:55883484-55884454	A549	lung:	n/a	n/a
23	POLR2A	chr19:55883874-55884018	K562	blood:	n/a	n/a
24	POLR2A	chr19:55883364-55884683	Hela-S3	cervix:	n/a	n/a
25	PBX3	chr19:55883251-55886358	A549	lung:	n/a	chr19:55885703-55885712
26	TFAP2A	chr19:55883403-55884582	Hela-S3	cervix:	n/a	chr19:55883830-55883840 chr19:55883830-55883840 chr19:55883830-55883840 chr19:55884362-55884371 chr19:55884396-55884404 chr19:55884393-55884407 chr19:55884391-55884406 chr19:55884393-55884407 chr19:55883830-55883840 chr19:55884416-55884428 chr19:55884279-55884288
27	POLR2A	chr19:55883643-55884497	MCF-7	breast:	n/a	n/a
28	SP1	chr19:55883408-55886397	A549	lung:	n/a	chr19:55885846-55885860 chr19:55885852-55885864 chr19:55885853-55885867 chr19:55885846-55885856 chr19:55883767-55883779 chr19:55885853-55885863 chr19:55883838-55883852 chr19:55883764-55883778 chr19:55885846-55885855 chr19:55885845-55885857 chr19:55885846-55885856 chr19:55885847-55885856 chr19:55885852-55885864 chr19:55883768-55883777 chr19:55885846-55885855 chr19:55885845-55885857 chr19:55885854-55885863
29	BCL3	chr19:55883381-55884667	A549	lung:	n/a	chr19:55884199-55884208
30	POLR2A	chr19:55883255-55886244	MCF10A-Er-Src	breast:	n/a	n/a
31	ELF1	chr19:55883711-55884503	A549	lung:	n/a	chr19:55884272-55884281
32	ZBTB7A	chr19:55883594-55884548	ECC-1	luminal epithelium:	n/a	chr19:55884187-55884195
33	GATA3	chr19:55883430-55884660	A549	lung:	n/a	n/a
34	POLR2A	chr19:55883395-55884320	Raji	blood:	n/a	n/a
35	POLR2A	chr19:55883331-55884512	MCF-7	breast:	n/a	n/a
36	ZBTB7A	chr19:55883805-55884532	K562	blood:	n/a	chr19:55884187-55884195
37	TCF12	chr19:55883223-55886437	A549	lung:	n/a	chr19:55885328-55885337 chr19:55884424-55884431 chr19:55885912-55885921 chr19:55884422-55884432
38	EP300	chr19:55883560-55886411	A549	lung:	n/a	chr19:55885754-55885770 chr19:55886005-55886012
39	GATA3	chr19:55883431-55886343	A549	lung:	n/a	n/a
40	NR3C1	chr19:55883559-55884521	A549	lung:	n/a	chr19:55884279-55884288 chr19:55884362-55884371 chr19:55883681-55883694 chr19:55883672-55883685
41	GATA3	chr19:55883693-55884189	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55877367..55879452-chr19:55882812..55884383,2	K562	blood:
2	chr19:55880381..55884285-chr19:55886063..55890457,4	K562	blood:
3	chr19:55876167..55879423-chr19:55882046..55885127,4	K562	blood:

Variant related genes	Relation type
TMEM190	TF binding region
IL11	TF binding region
ENSG00000269275	Chromatin interaction
ENSG00000160472	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1126757	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs12980914	0.88[EUR][1000 genomes]
rs35791293	0.80[ASN][1000 genomes]
rs4252546	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
4	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
5	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
6	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
7	nsv912461	chr19:55845386-55897327	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
8	nsv470162	chr19:55845386-55902257	Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
9	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
10	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
11	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
12	esv1799638	chr19:55850652-55883879	Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking 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 miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv516199	chr19:55854313-55901099	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
14	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
15	nsv912468	chr19:55872591-55883879	Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
16	nsv912469	chr19:55872591-55888598	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
17	nsv912470	chr19:55872591-55897170	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	79 gene(s)	inside rSNPs	diseases
18	nsv912472	chr19:55873726-55888598	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
19	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
20	nsv912474	chr19:55874986-55883879	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
21	nsv912475	chr19:55874986-55888598	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
22	nsv544085	chr19:55875808-55911275	Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
23	nsv912476	chr19:55876747-55897327	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	91 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55881400-55894800	Weak transcription	Right Atrium	heart
2	chr19:55882400-55885400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr19:55882600-55884000	Weak transcription	HSMM	muscle
4	chr19:55882600-55884000	Weak transcription	Osteobl	bone
5	chr19:55882600-55885200	Weak transcription	HSMMtube	muscle
6	chr19:55882600-55885400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr19:55882800-55885200	Weak transcription	NHLF	lung
8	chr19:55883200-55884400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
9	chr19:55883200-55885400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:55883200-55886400	Enhancers	NH-A	brain
11	chr19:55883200-55890000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:55883400-55884000	Bivalent Enhancer	HepG2	liver
13	chr19:55883400-55884400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr19:55883400-55885400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr19:55883400-55885600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:55883600-55884000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:55883600-55884000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
18	chr19:55883600-55884000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
19	chr19:55883600-55884000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:55883600-55884200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:55883600-55884400	Bivalent Enhancer	Placenta	Placenta
22	chr19:55883600-55884400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr19:55883600-55884600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr19:55883600-55884800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:55883600-55885000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:55883600-55885200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:55883600-55885600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:55883600-55887200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
29	chr19:55883800-55884000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr19:55883800-55884000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
31	chr19:55883800-55884000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
32	chr19:55883800-55884000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
33	chr19:55883800-55884000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:55883800-55884000	Bivalent/Poised TSS	Right Ventricle	heart
35	chr19:55883800-55884000	Flanking Active TSS	A549	lung
36	chr19:55883800-55884000	Enhancers	Hela-S3	cervix
37	chr19:55883800-55884400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
38	chr19:55883800-55884800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:55883800-55884800	Enhancers	HMEC	breast
40	chr19:55883800-55885400	Enhancers	Primary hematopoietic stem cells	blood
41	chr19:55883800-55885800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:55883800-55885800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:55883800-55886200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr19:55883800-55886400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr19:55883800-55888800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:55883800-55889200	Bivalent Enhancer	Fetal Stomach	stomach

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