Variant report

Variant	rs12980914
Chromosome Location	chr19:55883509-55883510
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	POLR2A	chr19:55883488-55883973	Hela-S3	cervix:	n/a	n/a
4	PBX3	chr19:55883291-55884712	A549	lung:	n/a	n/a
5	POLR2A	chr19:55883178-55886272	IMR90	lung:	n/a	n/a
6	MAZ	chr19:55883230-55886457	IMR90	lung:	n/a	n/a
7	REST	chr19:55883305-55883603	A549	lung:	n/a	n/a
8	FOSL2	chr19:55883380-55884643	A549	lung:	n/a	chr19:55884279-55884289 chr19:55884362-55884372 chr19:55884277-55884288 chr19:55884363-55884371 chr19:55884362-55884372
9	MAX	chr19:55883227-55884650	A549	lung:	n/a	n/a
10	TFAP2C	chr19:55883403-55884560	Hela-S3	cervix:	n/a	chr19:55884414-55884429 chr19:55884391-55884406
11	POLR2A	chr19:55883239-55883740	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:55883254-55886288	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr19:55883484-55884454	A549	lung:	n/a	n/a
14	POLR2A	chr19:55883364-55884683	Hela-S3	cervix:	n/a	n/a
15	PBX3	chr19:55883251-55886358	A549	lung:	n/a	chr19:55885703-55885712
16	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
17	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
18	BCL3	chr19:55883381-55884667	A549	lung:	n/a	chr19:55884199-55884208
19	POLR2A	chr19:55883255-55886244	MCF10A-Er-Src	breast:	n/a	n/a
20	GATA3	chr19:55883430-55884660	A549	lung:	n/a	n/a
21	POLR2A	chr19:55883395-55884320	Raji	blood:	n/a	n/a
22	POLR2A	chr19:55883331-55884512	MCF-7	breast:	n/a	n/a
23	TCF12	chr19:55883223-55886437	A549	lung:	n/a	chr19:55885328-55885337 chr19:55884424-55884431 chr19:55885912-55885921 chr19:55884422-55884432
24	GATA3	chr19:55883431-55886343	A549	lung:	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:
4	chr19:55865908..55868131-chr19:55880960..55883611,2	MCF-7	breast:
5	chr19:55872617..55875125-chr19:55881370..55883672,2	K562	blood:

Variant related genes	Relation type
TMEM190	TF binding region
IL11	TF binding region
ENSG00000269275	Chromatin interaction
ENSG00000160471	Chromatin interaction
ENSG00000160472	Chromatin interaction
ENSG00000180043	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1042505	0.88[ASN][1000 genomes]
rs11666163	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11666276	0.86[ASN][1000 genomes]
rs2298885	0.86[ASN][1000 genomes]
rs4252546	0.88[EUR][1000 genomes]
rs4252557	0.93[ASN][1000 genomes]
rs4252561	0.88[ASN][1000 genomes]
rs62128183	0.96[ASN][1000 genomes]
rs62128184	0.96[ASN][1000 genomes]
rs6509940	0.88[EUR][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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55881400-55894800	Weak transcription	Right Atrium	heart
2	chr19:55882400-55883800	Weak transcription	Right Ventricle	heart
3	chr19:55882400-55883800	Weak transcription	HMEC	breast
4	chr19:55882400-55885400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:55882600-55883600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:55882600-55883600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:55882600-55884000	Weak transcription	HSMM	muscle
8	chr19:55882600-55884000	Weak transcription	Osteobl	bone
9	chr19:55882600-55885200	Weak transcription	HSMMtube	muscle
10	chr19:55882600-55885400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr19:55882800-55883600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:55882800-55883800	Enhancers	A549	lung
13	chr19:55882800-55885200	Weak transcription	NHLF	lung
14	chr19:55883200-55884400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
15	chr19:55883200-55885400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:55883200-55886400	Enhancers	NH-A	brain
17	chr19:55883200-55890000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:55883400-55883600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr19:55883400-55883600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:55883400-55883600	Bivalent Enhancer	Fetal Kidney	kidney
21	chr19:55883400-55883600	Bivalent Enhancer	Hela-S3	cervix
22	chr19:55883400-55883800	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
23	chr19:55883400-55883800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
24	chr19:55883400-55883800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:55883400-55884000	Bivalent Enhancer	HepG2	liver
26	chr19:55883400-55884400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:55883400-55885400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:55883400-55885600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived

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