Variant report

Variant	rs1865093
Chromosome Location	chr19:39936134-39936135
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	chr19:39935561-39936863	A549	lung:	n/a	chr19:39935741-39935755
2	ZBTB33	chr19:39935921-39936484	GM12878	blood:	n/a	chr19:39936192-39936207 chr19:39936195-39936205 chr19:39936197-39936206
3	CTCF	chr19:39936040-39936190	Caco-2	colon:	n/a	n/a
4	TCF12	chr19:39935770-39936904	A549	lung:	n/a	n/a
5	SP1	chr19:39936027-39936408	GM12878	blood:	n/a	n/a
6	NFIC	chr19:39935924-39936349	HepG2	liver:	n/a	n/a
7	MYC	chr19:39936024-39936428	HepG2	liver:	n/a	n/a
8	TAF1	chr19:39935776-39936726	ECC-1	luminal epithelium:	n/a	n/a
9	ELK1	chr19:39935996-39936663	GM12878	blood:	n/a	n/a
10	FOXM1	chr19:39935688-39936681	GM12878	blood:	n/a	n/a
11	SIN3AK20	chr19:39935907-39936499	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:39935644-39936686	GM12892	blood:	n/a	n/a
13	ZBTB33	chr19:39935905-39936529	HCT-116	colon:	n/a	chr19:39936192-39936207 chr19:39936195-39936205 chr19:39936197-39936206
14	FOXA1	chr19:39936051-39936310	T-47D	breast:	n/a	n/a
15	GATA1	chr19:39935654-39936870	PBDE	blood:	n/a	n/a
16	SRF	chr19:39936079-39936326	HepG2	liver:	n/a	n/a
17	ZBTB33	chr19:39935999-39936342	HepG2	liver:	n/a	chr19:39936192-39936207 chr19:39936195-39936205 chr19:39936197-39936206
18	MAX	chr19:39935922-39936664	Hela-S3	cervix:	n/a	n/a
19	YY1	chr19:39935552-39936458	H1-hESC	embryonic stem cell:	n/a	chr19:39936123-39936133 chr19:39936122-39936130 chr19:39936118-39936134 chr19:39936086-39936100 chr19:39936111-39936133
20	ELF1	chr19:39935936-39936466	HepG2	liver:	n/a	chr19:39936410-39936419 chr19:39936033-39936045
21	SIX5	chr19:39935964-39936345	K562	blood:	n/a	chr19:39936315-39936324
22	POLR2A	chr19:39935680-39936625	GM12892	blood:	n/a	n/a
23	CREB1	chr19:39935789-39936566	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:39935266-39936619	HUVEC	blood vessel:	n/a	n/a
25	GTF2F1	chr19:39935539-39936429	H1-hESC	embryonic stem cell:	n/a	n/a
26	E2F4	chr19:39935993-39936324	MCF10A-Er-Src	breast:	n/a	n/a
27	MAX	chr19:39935871-39936585	H1-hESC	embryonic stem cell:	n/a	n/a
28	CHD2	chr19:39935865-39936662	HepG2	liver:	n/a	chr19:39936197-39936206
29	JUND	chr19:39935980-39936360	HepG2	liver:	n/a	n/a
30	POLR2A	chr19:39935800-39936714	GM18505	blood:	n/a	n/a
31	REST	chr19:39935115-39937132	A549	lung:	n/a	chr19:39936465-39936478
32	ATF3	chr19:39935679-39936692	A549	lung:	n/a	n/a
33	POLR2A	chr19:39935607-39936643	MCF-7	breast:	n/a	n/a
34	ZBTB33	chr19:39935906-39936398	HepG2	liver:	n/a	chr19:39936192-39936207 chr19:39936195-39936205 chr19:39936197-39936206
35	MAX	chr19:39935886-39936785	MCF-7	breast:	n/a	n/a
36	BRCA1	chr19:39935501-39936615	Hela-S3	cervix:	n/a	chr19:39936197-39936206
37	POLR2A	chr19:39935859-39936481	K562	blood:	n/a	n/a
38	HCFC1	chr19:39935163-39937047	Hela-S3	cervix:	n/a	n/a
39	PML	chr19:39935837-39936610	MCF-7	breast:	n/a	n/a
40	MEF2A	chr19:39935889-39936428	GM12878	blood:	n/a	n/a
41	ELF1	chr19:39935713-39936579	GM12878	blood:	n/a	chr19:39936410-39936419 chr19:39936033-39936045
42	CREB1	chr19:39935810-39936734	K562	blood:	n/a	n/a
43	FOS	chr19:39936124-39936323	MCF10A-Er-Src	breast:	n/a	n/a
44	YY1	chr19:39935869-39936403	K562	blood:	n/a	chr19:39936123-39936133 chr19:39936122-39936130 chr19:39936118-39936134 chr19:39936086-39936100 chr19:39936111-39936133
45	TBP	chr19:39935658-39936476	Hela-S3	cervix:	n/a	n/a
46	GATA3	chr19:39935814-39936308	T-47D	breast:	n/a	n/a
47	MAX	chr19:39935933-39936437	K562	blood:	n/a	n/a
48	EGR1	chr19:39936102-39936362	GM12878	blood:	n/a	chr19:39936256-39936270
49	POLR2A	chr19:39935879-39936461	SK-N-SH	brain:	n/a	n/a
50	WRNIP1	chr19:39935500-39936847	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39935867..39937651-chr19:40022035..40024212,2	MCF-7	breast:
2	chr19:39934417..39936200-chr19:40029570..40032204,2	MCF-7	breast:
3	chr19:39934545..39937545-chr19:40023023..40025430,4	MCF-7	breast:
4	chr19:39935872..39937858-chr19:40003816..40005942,2	MCF-7	breast:
5	chr1:28974685..28975549-chr19:39935889..39936794,2	Hela-S3	cervix:
6	chr1:45187114..45187776-chr19:39935987..39936543,2	Hela-S3	cervix:
7	chr19:39934091..39937114-chr19:39969895..39972879,3	K562	blood:
8	chr12:7053697..7055521-chr19:39934988..39936687,2	MCF-7	breast:
9	chr19:39934676..39937838-chr19:39970025..39973557,7	MCF-7	breast:
10	chr19:39934091..39937562-chr19:39970121..39972977,5	K562	blood:
11	chr19:39933642..39937454-chr19:40029470..40032868,6	MCF-7	breast:
12	chr19:39930372..39932549-chr19:39934536..39937097,4	K562	blood:
13	chr19:39934791..39938517-chr19:40022234..40026334,4	K562	blood:
14	chr19:39831465..39834764-chr19:39935836..39937934,3	K562	blood:
15	chr19:39935648..39936578-chr5:14664034..14664744,2	Hela-S3	cervix:
16	chr10:99400241..99400891-chr19:39935858..39936665,2	Hela-S3	cervix:
17	chr19:39935972..39937694-chr19:39965602..39968199,3	K562	blood:
18	chr19:39934619..39937838-chr19:39970480..39972998,6	MCF-7	breast:
19	chr19:39903188..39905724-chr19:39934407..39937965,7	MCF-7	breast:
20	chr19:39924469..39929022-chr19:39934307..39938518,21	MCF-7	breast:

Variant related genes	Relation type
SUPT5H	TF binding region
ENSG00000272173	Chromatin interaction
ENSG00000105197	Chromatin interaction
ENSG00000176401	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000186838	Chromatin interaction
ENSG00000270103	Chromatin interaction
ENSG00000269584	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000269792	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000105193	Chromatin interaction
ENSG00000090924	Chromatin interaction
ENSG00000130755	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000155252	Chromatin interaction
ENSG00000261360	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10406924	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10425652	1.00[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs1865090	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786950	1.00[CEU][hapmap];0.89[TSI][hapmap]
rs4802032	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4802033	1.00[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs4803238	0.90[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4803248	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
3	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1865093	IL28A	cis	lymphoblastoid	seeQTL
rs1865093	RPS16	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39934800-39937000	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr19:39934800-39937000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr19:39934800-39937000	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr19:39934800-39937000	Active TSS	A549	lung
5	chr19:39934800-39937200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr19:39935000-39936200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr19:39935000-39936400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:39935000-39936400	Active TSS	Brain Germinal Matrix	brain
9	chr19:39935000-39936600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:39935000-39936600	Active TSS	Fetal Brain Female	brain
11	chr19:39935000-39936800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr19:39935000-39936800	Active TSS	Muscle Satellite Cultured Cells	--
13	chr19:39935000-39936800	Active TSS	HMEC	breast
14	chr19:39935000-39936800	Active TSS	NHEK	skin
15	chr19:39935000-39937000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:39935000-39937000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:39935000-39937000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:39935000-39937000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:39935000-39937000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr19:39935000-39937000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr19:39935000-39937000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:39935000-39937000	Active TSS	Psoas Muscle	Psoas
23	chr19:39935000-39937000	Active TSS	Rectal Smooth Muscle	rectum
24	chr19:39935000-39937000	Active TSS	Right Ventricle	heart
25	chr19:39935000-39937200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:39935000-39937400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:39935000-39937400	Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr19:39935000-39937400	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr19:39935000-39937400	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr19:39935000-39937600	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr19:39935200-39936400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:39935200-39936400	Active TSS	Colonic Mucosa	Colon
33	chr19:39935200-39936600	Active TSS	Brain Substantia Nigra	brain
34	chr19:39935200-39936600	Active TSS	Lung	lung
35	chr19:39935200-39936600	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr19:39935200-39936800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:39935200-39936800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:39935200-39936800	Active TSS	Primary T cells from cord blood	blood
39	chr19:39935200-39936800	Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr19:39935200-39936800	Active TSS	Brain Cingulate Gyrus	brain
41	chr19:39935200-39936800	Active TSS	Brain Hippocampus Middle	brain
42	chr19:39935200-39936800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:39935200-39936800	Active TSS	Colon Smooth Muscle	Colon
44	chr19:39935200-39936800	Active TSS	Fetal Lung	lung
45	chr19:39935200-39937000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:39935200-39937000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:39935200-39937000	Active TSS	Aorta	Aorta
48	chr19:39935200-39937000	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr19:39935200-39937000	Active TSS	Esophagus	oesophagus
50	chr19:39935200-39937000	Active TSS	Fetal Muscle Trunk	muscle

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