Variant report

Variant	rs3761032
Chromosome Location	chr19:18721314-18721315
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	chr19:18721001-18721600	HepG2	liver:	n/a	n/a
2	HNF4G	chr19:18721075-18722070	HepG2	liver:	n/a	chr19:18722013-18722026 chr19:18721822-18721829 chr19:18722012-18722025 chr19:18722013-18722025 chr19:18721817-18721833 chr19:18722013-18722025 chr19:18721208-18721216 chr19:18722008-18722030 chr19:18721504-18721518 chr19:18722012-18722025
3	MAZ	chr19:18721132-18721817	HepG2	liver:	n/a	chr19:18721650-18721660
4	NFIC	chr19:18721249-18721592	HepG2	liver:	n/a	n/a
5	ZBTB7A	chr19:18721308-18721930	HepG2	liver:	n/a	n/a
6	MYBL2	chr19:18721251-18721803	HepG2	liver:	n/a	n/a
7	NFIC	chr19:18721251-18722067	HepG2	liver:	n/a	n/a
8	TEAD4	chr19:18721006-18721347	HepG2	liver:	n/a	n/a
9	RXRA	chr19:18721114-18721968	HepG2	liver:	n/a	n/a
10	FOSL2	chr19:18721307-18721762	HepG2	liver:	n/a	chr19:18721738-18721747 chr19:18721653-18721662 chr19:18721654-18721663 chr19:18721652-18721661
11	NR2F2	chr19:18720900-18722132	HepG2	liver:	n/a	chr19:18722014-18722029
12	EP300	chr19:18721120-18721606	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:18721172-18721601	HepG2	liver:	n/a	n/a
14	HNF4A	chr19:18721126-18721651	HepG2	liver:	n/a	chr19:18721208-18721216 chr19:18721504-18721518
15	FOXA2	chr19:18720946-18721588	HepG2	liver:	n/a	n/a
16	ZBTB7A	chr19:18721174-18723265	ECC-1	luminal epithelium:	n/a	chr19:18722623-18722631
17	MXI1	chr19:18721290-18721570	HepG2	liver:	n/a	n/a
18	EP300	chr19:18721142-18723056	ECC-1	luminal epithelium:	n/a	chr19:18722743-18722759 chr19:18722567-18722583 chr19:18722742-18722758 chr19:18721667-18721676 chr19:18721839-18721855 chr19:18722746-18722762
19	POLR2A	chr19:18721137-18721617	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:18719758-18723372	HepG2	liver:	n/a	n/a
21	ELF1	chr19:18721093-18721961	HepG2	liver:	n/a	n/a
22	RCOR1	chr19:18721191-18721585	HepG2	liver:	n/a	n/a
23	HEY1	chr19:18721074-18721679	HepG2	liver:	n/a	chr19:18721659-18721674
24	POLR2A	chr19:18721234-18721577	HepG2	liver:	n/a	n/a
25	TCF12	chr19:18721164-18723022	ECC-1	luminal epithelium:	n/a	chr19:18722354-18722361
26	ZBTB7A	chr19:18720992-18722058	HepG2	liver:	n/a	n/a
27	HDAC2	chr19:18720987-18722019	HepG2	liver:	n/a	n/a
28	CEBPB	chr19:18721234-18721377	HepG2	liver:	n/a	n/a
29	CEBPD	chr19:18721036-18722077	HepG2	liver:	n/a	n/a
30	TCF12	chr19:18721314-18721867	HepG2	liver:	n/a	n/a
31	NFIC	chr19:18721290-18722073	ECC-1	luminal epithelium:	n/a	n/a
32	MYBL2	chr19:18720977-18721733	HepG2	liver:	n/a	n/a
33	FOXA1	chr19:18720983-18721331	HepG2	liver:	n/a	n/a
34	HNF4A	chr19:18721049-18721687	HepG2	liver:	n/a	chr19:18721208-18721216 chr19:18721504-18721518
35	HNF4A	chr19:18721058-18721933	HepG2	liver:	n/a	chr19:18721822-18721829 chr19:18721817-18721833 chr19:18721208-18721216 chr19:18721504-18721518
36	TBP	chr19:18721060-18721500	HepG2	liver:	n/a	n/a
37	RXRA	chr19:18721243-18721995	HepG2	liver:	n/a	n/a
38	YY1	chr19:18721132-18721999	HepG2	liver:	n/a	chr19:18721667-18721676 chr19:18721566-18721577 chr19:18721661-18721675 chr19:18721847-18721858 chr19:18721280-18721291
39	EP300	chr19:18720368-18722181	HepG2	liver:	n/a	chr19:18721667-18721676 chr19:18721839-18721855
40	ZBTB7A	chr19:18721115-18724078	ECC-1	luminal epithelium:	n/a	chr19:18722623-18722631
41	CTBP2	chr19:18721038-18721602	H1-hESC	embryonic stem cell:	n/a	n/a
42	SP1	chr19:18720956-18722007	HepG2	liver:	n/a	chr19:18721875-18721884 chr19:18721463-18721477 chr19:18721654-18721668 chr19:18721752-18721766 chr19:18721751-18721763 chr19:18721435-18721449
43	POLR2A	chr19:18721136-18721535	HepG2	liver:	n/a	n/a
44	RFX5	chr19:18721237-18721486	HepG2	liver:	n/a	n/a
45	TCF12	chr19:18721193-18722490	ECC-1	luminal epithelium:	n/a	chr19:18722354-18722361
46	EP300	chr19:18721312-18722088	ECC-1	luminal epithelium:	n/a	chr19:18721667-18721676 chr19:18721839-18721855
47	HEY1	chr19:18721023-18721564	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:18720681..18723578-chr19:18792529..18794058,2	K562	blood:
2	chr19:18719600..18721808-chr19:18793150..18795640,2	MCF-7	breast:
3	chr19:18714423..18716001-chr19:18720923..18723094,2	K562	blood:
4	chr19:18715795..18719274-chr19:18719391..18724999,7	MCF-7	breast:
5	chr19:18714258..18716711-chr19:18719461..18722423,3	K562	blood:
6	chr19:18713204..18718867-chr19:18719015..18725496,7	MCF-7	breast:
7	chr19:18700084..18702080-chr19:18719094..18721979,3	K562	blood:

Variant related genes	Relation type
CRLF1	TF binding region
TMEM59L	TF binding region
ENSG00000105696	Chromatin interaction
ENSG00000105662	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000006016	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10409392	0.81[JPT][hapmap]
rs10415560	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1043192	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12609505	0.81[JPT][hapmap]
rs1468475	0.81[JPT][hapmap]
rs1862645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1966500	0.81[ASN][1000 genomes]
rs2057649	0.90[JPT][hapmap]
rs2074175	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs2079015	0.90[JPT][hapmap]
rs2238650	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283616	0.81[JPT][hapmap]
rs2302055	0.81[JPT][hapmap]
rs2314664	0.90[JPT][hapmap]
rs2314665	0.90[JPT][hapmap]
rs2314666	0.86[JPT][hapmap]
rs3170474	0.88[CEU][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs4808137	0.81[JPT][hapmap]
rs4808138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4808823	0.90[JPT][hapmap]
rs4808824	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808835	0.87[AMR][1000 genomes]
rs4808837	0.80[ASN][1000 genomes]
rs4808838	0.80[AMR][1000 genomes]
rs4808839	0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs6417264	0.89[EUR][1000 genomes]
rs6510993	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6554	0.81[JPT][hapmap]
rs709679	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7248037	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7250192	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250623	0.84[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7252198	0.88[EUR][1000 genomes]
rs7256319	0.92[CEU][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs7259557	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7359896	0.82[AMR][1000 genomes]
rs7648	0.81[JPT][hapmap]
rs916791	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911287	chr19:18699333-18727913	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv911288	chr19:18700047-18739497	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
11	nsv911291	chr19:18701499-18726856	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
12	nsv911292	chr19:18701499-18731658	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3761032	AP1M1	cis	parietal	SCAN
rs3761032	KIAA0892	cis	cerebellum	SCAN
rs3761032	UBA52	cis	lymphoblastoid	seeQTL
rs3761032	NDUFA13	cis	parietal	SCAN
rs3761032	HAPLN4	cis	parietal	SCAN
rs3761032	PGLS	cis	parietal	SCAN
rs3761032	UNC13A	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18718400-18721400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
2	chr19:18718800-18721400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:18718800-18721400	Flanking Active TSS	HepG2	liver
4	chr19:18718800-18721800	Weak transcription	Right Atrium	heart
5	chr19:18719000-18721400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:18719000-18721400	Weak transcription	Pancreas	Pancrea
7	chr19:18719400-18721400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:18720200-18721400	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
9	chr19:18720400-18721400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
10	chr19:18720400-18721400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:18720600-18721400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
12	chr19:18720600-18723000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:18720600-18723200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr19:18720600-18723200	Bivalent Enhancer	Fetal Muscle Leg	muscle
15	chr19:18720800-18721600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
16	chr19:18720800-18722800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:18721000-18721400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:18721000-18721600	Bivalent Enhancer	Fetal Lung	lung
19	chr19:18721000-18722600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
20	chr19:18721000-18722600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:18721000-18722800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr19:18721000-18723000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:18721000-18723200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:18721000-18723600	Enhancers	Lung	lung
25	chr19:18721200-18721400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
26	chr19:18721200-18721400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
27	chr19:18721200-18721400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
28	chr19:18721200-18721400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:18721200-18721400	Bivalent Enhancer	Esophagus	oesophagus
30	chr19:18721200-18721600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
31	chr19:18721200-18722000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
32	chr19:18721200-18722000	Bivalent Enhancer	Stomach Smooth Muscle	stomach
33	chr19:18721200-18722200	Enhancers	HSMM	muscle
34	chr19:18721200-18722400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
35	chr19:18721200-18723000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:18721200-18723000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
37	chr19:18721200-18723400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:18721200-18723400	Bivalent Enhancer	HUVEC	blood vessel
39	chr19:18721200-18724400	Bivalent Enhancer	Placenta	Placenta

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