Variant report

Variant	rs7258904
Chromosome Location	chr19:55885584-55885585
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	FOSL2	chr19:55885381-55886329	A549	lung:	n/a	chr19:55885416-55885425 chr19:55885848-55885857
2	EP300	chr19:55883393-55886386	A549	lung:	n/a	chr19:55885754-55885770 chr19:55886005-55886012
3	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
4	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
5	REST	chr19:55885077-55886288	A549	lung:	n/a	chr19:55885486-55885496 chr19:55885830-55885843 chr19:55885934-55885944 chr19:55885825-55885838
6	HMGN3	chr19:55885520-55885695	K562	blood:	n/a	n/a
7	POLR2A	chr19:55884519-55886091	MCF-7	breast:	n/a	n/a
8	ZBTB7A	chr19:55885566-55885829	K562	blood:	n/a	chr19:55885806-55885814
9	YY1	chr19:55885352-55885831	A549	lung:	n/a	chr19:55885746-55885757
10	MAX	chr19:55885302-55886261	A549	lung:	n/a	n/a
11	NR3C1	chr19:55885391-55885977	A549	lung:	n/a	chr19:55885672-55885679
12	POLR2A	chr19:55883178-55886272	IMR90	lung:	n/a	n/a
13	NR3C1	chr19:55885507-55885780	A549	lung:	n/a	chr19:55885672-55885679
14	MAZ	chr19:55883230-55886457	IMR90	lung:	n/a	n/a
15	EBF1	chr19:55885556-55885799	GM12878	blood:	n/a	chr19:55885709-55885720 chr19:55885708-55885721 chr19:55885710-55885719
16	JUND	chr19:55885414-55886340	A549	lung:	n/a	chr19:55885416-55885425 chr19:55885848-55885857
17	POLR2A	chr19:55885522-55885888	ECC-1	luminal epithelium:	n/a	n/a
18	BCL3	chr19:55884746-55886219	A549	lung:	n/a	n/a
19	SIX5	chr19:55884801-55885958	A549	lung:	n/a	n/a
20	FOXA2	chr19:55884971-55886313	A549	lung:	n/a	n/a
21	SIN3AK20	chr19:55884905-55886071	A549	lung:	n/a	n/a
22	BCL3	chr19:55885019-55886309	A549	lung:	n/a	n/a
23	POLR2A	chr19:55885553-55885801	ProgFib	skin:	n/a	n/a
24	ZBTB7A	chr19:55885506-55886213	ECC-1	luminal epithelium:	n/a	chr19:55885806-55885814
25	USF1	chr19:55885468-55886090	A549	lung:	n/a	chr19:55885974-55885990
26	FOSL2	chr19:55885521-55886103	A549	lung:	n/a	chr19:55885848-55885857
27	GATA3	chr19:55885314-55886370	A549	lung:	n/a	n/a
28	REST	chr19:55885175-55886141	A549	lung:	n/a	chr19:55885486-55885496 chr19:55885830-55885843 chr19:55885934-55885944 chr19:55885825-55885838
29	CHD2	chr19:55885117-55886019	Hela-S3	cervix:	n/a	n/a
30	SIN3AK20	chr19:55885369-55885786	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr19:55885374-55885823	A549	lung:	n/a	n/a
32	POLR2A	chr19:55884946-55886214	A549	lung:	n/a	n/a
33	SIN3A	chr19:55885279-55885839	H1-hESC	embryonic stem cell:	n/a	chr19:55885825-55885838
34	CREB1	chr19:55885443-55886240	A549	lung:	n/a	n/a
35	CEBPB	chr19:55885484-55886052	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr19:55883254-55886288	MCF10A-Er-Src	breast:	n/a	n/a
37	MAX	chr19:55884744-55886356	A549	lung:	n/a	n/a
38	ATF3	chr19:55885287-55886087	A549	lung:	n/a	chr19:55885847-55885856 chr19:55885736-55885750
39	POLR2A	chr19:55885578-55885823	A549	lung:	n/a	n/a
40	SMC3	chr19:55885290-55885825	Hela-S3	cervix:	n/a	chr19:55885474-55885484
41	PBX3	chr19:55883251-55886358	A549	lung:	n/a	chr19:55885703-55885712
42	POLR2A	chr19:55885519-55886113	PANC-1	pancreas:	n/a	n/a
43	POLR2A	chr19:55884744-55886041	MCF-7	breast:	n/a	n/a
44	NR3C1	chr19:55885365-55885966	A549	lung:	n/a	chr19:55885672-55885679
45	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
46	ELF1	chr19:55885003-55886114	A549	lung:	n/a	chr19:55885939-55885951 chr19:55885650-55885662
47	POLR2A	chr19:55883255-55886244	MCF10A-Er-Src	breast:	n/a	n/a
48	NR3C1	chr19:55885495-55885827	A549	lung:	n/a	chr19:55885672-55885679
49	TCF12	chr19:55885024-55886213	A549	lung:	n/a	chr19:55885328-55885337 chr19:55885912-55885921
50	FOXA2	chr19:55885127-55886313	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55852315..55853947-chr19:55885473..55887551,2	K562	blood:
2	chr19:55851020..55853815-chr19:55885583..55887551,2	K562	blood:
3	chr19:55845491..55847724-chr19:55884578..55887231,2	MCF-7	breast:

Variant related genes	Relation type
TMEM190	TF binding region
IL11	TF binding region
ENSG00000267531	Chromatin interaction
ENSG00000133247	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10422041	0.87[AMR][1000 genomes]
rs10426501	0.82[AMR][1000 genomes]
rs1902608	0.91[AMR][1000 genomes]
rs2124918	0.80[ASN][1000 genomes]
rs2305787	0.82[AMR][1000 genomes]
rs4239592	1.00[AMR][1000 genomes]
rs4252556	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55881400-55894800	Weak transcription	Right Atrium	heart
2	chr19:55883200-55886400	Enhancers	NH-A	brain
3	chr19:55883200-55890000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:55883400-55885600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:55883600-55885600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:55883600-55887200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
7	chr19:55883800-55885800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:55883800-55885800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:55883800-55886200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
10	chr19:55883800-55886400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr19:55883800-55888800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:55883800-55889200	Bivalent Enhancer	Fetal Stomach	stomach
13	chr19:55884000-55885600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr19:55884000-55886200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr19:55884000-55886200	Flanking Active TSS	HepG2	liver
16	chr19:55884000-55890800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:55884200-55885800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:55884200-55885800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:55884400-55886400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:55884600-55886200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr19:55884800-55885800	Enhancers	Placenta Amnion	Placenta Amnion
22	chr19:55885000-55885600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:55885000-55885600	Enhancers	K562	blood
24	chr19:55885000-55885800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr19:55885000-55886000	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr19:55885000-55886200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr19:55885000-55886200	Bivalent Enhancer	Fetal Intestine Small	intestine
28	chr19:55885000-55886200	Bivalent Enhancer	Placenta	Placenta
29	chr19:55885000-55886200	Flanking Active TSS	A549	lung
30	chr19:55885000-55886200	Flanking Active TSS	Hela-S3	cervix
31	chr19:55885200-55885600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr19:55885200-55885600	Bivalent Enhancer	Fetal Kidney	kidney
33	chr19:55885200-55885800	Enhancers	Pancreas	Pancrea
34	chr19:55885200-55885800	Enhancers	HMEC	breast
35	chr19:55885200-55886000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
36	chr19:55885200-55886200	Bivalent Enhancer	Fetal Lung	lung
37	chr19:55885200-55886200	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr19:55885200-55886200	Enhancers	HSMMtube	muscle
39	chr19:55885200-55886200	Enhancers	NHLF	lung
40	chr19:55885200-55887400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:55885400-55885600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:55885400-55885600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr19:55885400-55885600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
44	chr19:55885400-55885600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
45	chr19:55885400-55885600	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr19:55885400-55885600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
47	chr19:55885400-55885600	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:55885400-55885600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
49	chr19:55885400-55885600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
50	chr19:55885400-55885600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--

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