Variant report

Variant	rs4252546
Chromosome Location	chr19:55882345-55882346
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	chr19:55882288-55882639	MCF10A-Er-Src	breast:	n/a	n/a
2	BCL3	chr19:55881146-55882765	A549	lung:	n/a	chr19:55881514-55881523 chr19:55881694-55881703 chr19:55881774-55881787
3	EP300	chr19:55881792-55882447	A549	lung:	n/a	chr19:55881892-55881908
4	MAZ	chr19:55879573-55882869	IMR90	lung:	n/a	chr19:55879994-55880003 chr19:55881877-55881887
5	POLR2A	chr19:55881183-55882692	Hela-S3	cervix:	n/a	n/a
6	EP300	chr19:55881654-55882364	A549	lung:	n/a	chr19:55881892-55881908
7	POLR2A	chr19:55882248-55882365	MCF-7	breast:	n/a	n/a
8	MAX	chr19:55881026-55882605	A549	lung:	n/a	chr19:55881877-55881887
9	CHD1	chr19:55879027-55882893	IMR90	lung:	n/a	chr19:55881216-55881226 chr19:55879790-55879800
10	PBX3	chr19:55879930-55882619	A549	lung:	n/a	chr19:55881464-55881473 chr19:55882591-55882600
11	SP1	chr19:55880984-55882544	A549	lung:	n/a	chr19:55881711-55881720 chr19:55882079-55882093 chr19:55881390-55881399 chr19:55881706-55881720 chr19:55881876-55881888 chr19:55881454-55881475 chr19:55881268-55881277
12	GATA3	chr19:55880452-55882631	A549	lung:	n/a	n/a
13	SP1	chr19:55881045-55882481	A549	lung:	n/a	chr19:55881711-55881720 chr19:55882079-55882093 chr19:55881390-55881399 chr19:55881706-55881720 chr19:55881876-55881888 chr19:55881454-55881475 chr19:55881268-55881277
14	TCF12	chr19:55881012-55882632	A549	lung:	n/a	n/a
15	POLR2A	chr19:55882315-55882351	Hela-S3	cervix:	n/a	n/a
16	MAX	chr19:55881040-55882460	A549	lung:	n/a	chr19:55881877-55881887
17	POLR2A	chr19:55882054-55882806	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr19:55873343-55882901	IMR90	lung:	n/a	n/a
19	SIN3AK20	chr19:55882100-55882445	A549	lung:	n/a	n/a
20	FOSL2	chr19:55881144-55882467	A549	lung:	n/a	chr19:55881920-55881928 chr19:55881918-55881930 chr19:55881872-55881881 chr19:55881883-55881892 chr19:55881463-55881472 chr19:55881919-55881930 chr19:55881876-55881885

No.	Distal block	Cell Line	Cell type
1	chr19:55853165..55857260-chr19:55879821..55883048,3	MCF-7	breast:
2	chr19:55856384..55859080-chr19:55879922..55882670,2	K562	blood:
3	chr19:55880381..55884285-chr19:55886063..55890457,4	K562	blood:
4	chr19:55880628..55883032-chr19:55887908..55889776,2	K562	blood:
5	chr19:55857308..55859712-chr19:55880679..55883398,3	MCF-7	breast:
6	chr19:55876167..55879423-chr19:55882046..55885127,4	K562	blood:
7	chr19:55865908..55868131-chr19:55880960..55883611,2	MCF-7	breast:
8	chr19:55849062..55852611-chr19:55879307..55883496,5	MCF-7	breast:
9	chr19:55864955..55867658-chr19:55880222..55883231,3	MCF-7	breast:
10	chr19:55872617..55875125-chr19:55881370..55883672,2	K562	blood:

Variant related genes	Relation type
IL11	TF binding region
ENSG00000269275	Chromatin interaction
ENSG00000180043	Chromatin interaction
ENSG00000160471	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000160472	Chromatin interaction
ENSG00000133247	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1126757	0.94[ASN][1000 genomes]
rs12980914	0.88[EUR][1000 genomes]
rs35117389	0.85[ASN][1000 genomes]
rs35791293	0.87[ASN][1000 genomes]
rs6509940	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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55880200-55882400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr19:55880600-55882400	Active TSS	HSMMtube	muscle
3	chr19:55881200-55882400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr19:55881200-55882400	Enhancers	Pancreas	Pancrea
5	chr19:55881200-55882600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:55881400-55882400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr19:55881400-55894800	Weak transcription	Right Atrium	heart
8	chr19:55881600-55882400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:55881600-55882400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr19:55881600-55882400	Bivalent Enhancer	Fetal Stomach	stomach
11	chr19:55881600-55882400	Active TSS	Right Ventricle	heart
12	chr19:55881800-55882400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:55881800-55882400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
14	chr19:55881800-55882600	Bivalent Enhancer	Hela-S3	cervix
15	chr19:55882000-55882400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:55882000-55882400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:55882000-55882400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
18	chr19:55882000-55882400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:55882000-55882400	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
20	chr19:55882000-55882400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:55882000-55882400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr19:55882000-55882400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:55882000-55882400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:55882000-55882400	Flanking Active TSS	HSMM	muscle
25	chr19:55882000-55882400	Flanking Active TSS	NHLF	lung
26	chr19:55882000-55882400	Flanking Active TSS	Osteobl	bone
27	chr19:55882000-55882600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:55882000-55882600	Flanking Active TSS	NH-A	brain
29	chr19:55882000-55882800	Flanking Active TSS	A549	lung
30	chr19:55882200-55882400	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:55882200-55882400	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
32	chr19:55882200-55882400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr19:55882200-55882400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
34	chr19:55882200-55882400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:55882200-55882400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:55882200-55882400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:55882200-55882400	Bivalent Enhancer	Lung	lung
38	chr19:55882200-55882400	Bivalent Enhancer	Stomach Mucosa	stomach
39	chr19:55882200-55882400	Flanking Bivalent TSS/Enh	HepG2	liver
40	chr19:55882200-55882400	Active TSS	HMEC	breast
41	chr19:55882200-55882400	Flanking Active TSS	NHDF-Ad	bronchial
42	chr19:55882200-55882400	Flanking Bivalent TSS/Enh	NHEK	skin
43	chr19:55882200-55882600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
44	chr19:55882200-55882600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
45	chr19:55882200-55882600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:55882200-55882600	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:55882200-55882600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
48	chr19:55882200-55882600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:55882200-55882600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
50	chr19:55882200-55882600	Bivalent Enhancer	Fetal Lung	lung

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