Variant report

Variant	rs2304176
Chromosome Location	chr19:38794895-38794896
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	GTF2F1	chr19:38794516-38794951	Hela-S3	cervix:	n/a	n/a
2	ZBTB33	chr19:38794168-38796572	A549	lung:	n/a	chr19:38795334-38795344
3	FOXA2	chr19:38794084-38795080	A549	lung:	n/a	n/a
4	POLR2A	chr19:38790918-38797378	PANC-1	pancreas:	n/a	n/a
5	SP1	chr19:38794293-38796291	HCT-116	colon:	n/a	chr19:38795161-38795175 chr19:38795711-38795723 chr19:38795219-38795228 chr19:38794828-38794840 chr19:38795689-38795703 chr19:38794562-38794576 chr19:38795682-38795696 chr19:38794828-38794840 chr19:38795689-38795698
6	YY1	chr19:38794598-38795084	ECC-1	luminal epithelium:	n/a	n/a
7	MYC	chr19:38794670-38794946	MCF-7	breast:	n/a	chr19:38794754-38794763
8	EP300	chr19:38794305-38796151	ECC-1	luminal epithelium:	n/a	chr19:38795382-38795398 chr19:38795409-38795422 chr19:38795147-38795163
9	MAZ	chr19:38794580-38794983	Hela-S3	cervix:	n/a	chr19:38794754-38794763
10	POLR2A	chr19:38794268-38796429	HCT-116	colon:	n/a	n/a
11	POLR2A	chr19:38794147-38796192	K562	blood:	n/a	n/a
12	POLR2A	chr19:38794383-38796359	K562	blood:	n/a	n/a
13	TEAD4	chr19:38794497-38795049	ECC-1	luminal epithelium:	n/a	n/a
14	ELF1	chr19:38794160-38796209	A549	lung:	n/a	n/a
15	GABPA	chr19:38794135-38795020	A549	lung:	n/a	n/a
16	POLR2A	chr19:38794272-38794944	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr19:38794325-38796169	MCF10A-Er-Src	breast:	n/a	n/a
18	TBP	chr19:38794616-38794974	Hela-S3	cervix:	n/a	n/a
19	TAF1	chr19:38794572-38795372	ECC-1	luminal epithelium:	n/a	n/a
20	FOSL2	chr19:38794609-38795194	HepG2	liver:	n/a	chr19:38794754-38794764 chr19:38794753-38794765 chr19:38794755-38794763
21	POLR2A	chr19:38794286-38796311	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYC	chr19:38794158-38796631	A549	lung:	n/a	chr19:38795351-38795364 chr19:38795352-38795363 chr19:38795349-38795364 chr19:38795353-38795362 chr19:38795352-38795363 chr19:38795353-38795363 chr19:38794754-38794763
23	POLR2A	chr19:38794375-38796435	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr19:38793963-38796680	A549	lung:	n/a	chr19:38796391-38796399 chr19:38795248-38795255
25	HNF4A	chr19:38794688-38795317	HepG2	liver:	n/a	chr19:38795120-38795135
26	FOSL2	chr19:38794499-38795031	MCF-7	breast:	n/a	chr19:38794754-38794764 chr19:38794753-38794765 chr19:38794755-38794763
27	FOS	chr19:38794602-38794922	MCF10A-Er-Src	breast:	n/a	chr19:38794754-38794764 chr19:38794753-38794765 chr19:38794755-38794763 chr19:38794753-38794764
28	POLR2A	chr19:38794683-38795032	H1-hESC	embryonic stem cell:	n/a	n/a
29	TEAD4	chr19:38794454-38795178	ECC-1	luminal epithelium:	n/a	n/a
30	FOS	chr19:38794574-38794946	MCF10A-Er-Src	breast:	n/a	chr19:38794754-38794764 chr19:38794753-38794765 chr19:38794755-38794763 chr19:38794753-38794764
31	JUND	chr19:38794420-38796112	A549	lung:	n/a	chr19:38794754-38794764 chr19:38794753-38794765 chr19:38794755-38794763
32	NR3C1	chr19:38794333-38795161	A549	lung:	n/a	n/a
33	POLR2A	chr19:38794314-38796386	K562	blood:	n/a	n/a
34	SP1	chr19:38794006-38796345	A549	lung:	n/a	chr19:38795161-38795175 chr19:38795711-38795723 chr19:38795219-38795228 chr19:38794828-38794840 chr19:38795689-38795703 chr19:38794562-38794576 chr19:38795682-38795696 chr19:38794828-38794840 chr19:38795689-38795698
35	GABPA	chr19:38794324-38795058	MCF-7	breast:	n/a	n/a
36	BHLHE40	chr19:38794338-38795860	A549	lung:	n/a	chr19:38794500-38794516 chr19:38795353-38795362 chr19:38795353-38795362 chr19:38795354-38795363
37	POLR2A	chr19:38794444-38795838	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr19:38794240-38796636	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr19:38794491-38794986	HUVEC	blood vessel:	n/a	n/a
40	YY1	chr19:38794549-38794976	HCT-116	colon:	n/a	n/a
41	CREB1	chr19:38794262-38796236	A549	lung:	n/a	n/a
42	JUND	chr19:38794302-38796622	A549	lung:	n/a	chr19:38794754-38794764 chr19:38794753-38794765 chr19:38794755-38794763
43	BRCA1	chr19:38794539-38794901	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr19:38794309-38795933	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr19:38794327-38796008	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr19:38794367-38796249	MCF-7	breast:	n/a	n/a
47	MAX	chr19:38794115-38796360	A549	lung:	n/a	chr19:38795351-38795364 chr19:38795352-38795363 chr19:38795349-38795364 chr19:38795353-38795362 chr19:38795352-38795363 chr19:38795353-38795363 chr19:38794754-38794763
48	TEAD4	chr19:38794595-38794997	H1-hESC	embryonic stem cell:	n/a	n/a
49	ATF3	chr19:38794088-38796300	A549	lung:	n/a	n/a
50	USF1	chr19:38794207-38796162	A549	lung:	n/a	chr19:38794500-38794516 chr19:38795353-38795362 chr19:38795353-38795362 chr19:38795354-38795363

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:38794845-38794895	AG09319	gingival:	n/a
2	chr19:38794845-38794895	SKMC	muscle:	n/a
3	chr19:38794845-38794895	GM12878	blood:	n/a
4	chr19:38794845-38794895	NB4	blood:	n/a
5	chr19:38794845-38794895	PANC-1	pancreas:	n/a
6	chr19:38794845-38794895	HCT-116	colon:	n/a
7	chr19:38794845-38794895	ECC-1	luminal epithelium:	n/a
8	chr19:38794845-38794895	NHBE	bronchial:	n/a
9	chr19:38794845-38794895	HIPEpiC	eye:	n/a
10	chr19:38794845-38794895	HepG2	liver:	n/a
11	chr19:38794845-38794895	SK-N-MC	brain:	n/a
12	chr19:38794845-38794895	AG09309	skin:	n/a
13	chr19:38794845-38794895	SK-N-SH_RA	brain:	n/a
14	chr19:38794845-38794895	PFSK-1	brain:	n/a
15	chr19:38794845-38794895	T-47D	breast:	n/a
16	chr19:38794845-38794895	IMR90	lung:	fetal
17	chr19:38794845-38794895	CMK	blood:	n/a
18	chr19:38794845-38794895	RPTEC	kidney:	n/a
19	chr19:38794845-38794895	HAEpiC	amniotic membrane:	n/a
20	chr19:38794845-38794895	NH-A	brain:	n/a
21	chr19:38794845-38794895	ovcar-3	ovarian:	n/a
22	chr19:38794845-38794895	HRPEpiC	eye:	n/a
23	chr19:38794845-38794895	SK-N-SH	brain:	n/a
24	chr19:38794845-38794895	AoSMC	blood vessel:	n/a
25	chr19:38794845-38794895	Hepatocyte	liver:	n/a
26	chr19:38794845-38794895	HL-60	blood:	n/a
27	chr19:38794845-38794895	MCF-7	breast:	n/a
28	chr19:38794845-38794895	LNCaP	prostate:	n/a
29	chr19:38794845-38794895	HEEpiC	esophagus:	n/a
30	chr19:38794845-38794895	MCF10A-Er-Src	breast:	n/a
31	chr19:38794845-38794895	A549	lung:	n/a
32	chr19:38794845-38794895	NT2-D1	testis:	n/a
33	chr19:38794845-38794895	AG04449	skin:	fetal
34	chr19:38794845-38794895	SAEC	small airway:	n/a
35	chr19:38794845-38794895	HMEC	breast:	n/a
36	chr19:38794845-38794895	NHDF-neo	bronchial:	n/a
37	chr19:38794845-38794895	BJ	skin:	n/a
38	chr19:38794845-38794895	HNPCEpiC	eye:	n/a
39	chr19:38794845-38794895	H1-hESC	embryonic stem cell:	embryo
40	chr19:38794845-38794895	HPAEpiC	pulmonary alveolar:	n/a
41	chr19:38794845-38794895	AG10803	skin:	n/a
42	chr19:38794845-38794895	HRCEpiC	kidney:	n/a
43	chr19:38794845-38794895	U87	brain:	n/a
44	chr19:38794845-38794895	PrEC	prostate:	n/a
45	chr19:38794845-38794895	Caco-2	colon:	n/a
46	chr19:38794845-38794895	Jurkat	blood:	n/a
47	chr19:38794845-38794895	AG04450	lung:	fetal
48	chr19:38794845-38794895	Hela-S3	cervix:	n/a
49	chr19:38794845-38794895	HCPEpiC	choroid plexus:	n/a
50	chr19:38794845-38794895	GM19239	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:245134044..245134798-chr19:38794839..38795559,2	Hela-S3	cervix:
2	chr19:38753031..38764322-chr19:38787496..38798494,54	MCF-7	breast:
3	chr19:38718266..38721870-chr19:38794040..38798765,4	MCF-7	breast:
4	chr19:38779327..38783351-chr19:38794485..38798006,3	K562	blood:
5	chr1:149223898..149224411-chr19:38794775..38795700,2	Hela-S3	cervix:
6	chr19:38794775..38795460-chr3:119814356..119814863,2	Hela-S3	cervix:
7	chr19:38794669..38796308-chr19:38799482..38801247,2	K562	blood:
8	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
9	chr19:38794216..38796351-chr19:38852337..38854290,3	MCF-7	breast:
10	chr14:64108540..64109428-chr19:38794685..38795598,2	Hela-S3	cervix:
11	chr19:38794641..38795623-chr7:73867369..73868176,2	Hela-S3	cervix:
12	chr19:38793475..38795482-chr19:38826442..38828638,2	K562	blood:
13	chr19:38791989..38796796-chr19:38825093..38829391,7	MCF-7	breast:
14	chr19:38784964..38786694-chr19:38794356..38796889,2	K562	blood:
15	chr19:38744771..38747370-chr19:38793659..38796631,3	MCF-7	breast:

Variant related genes	Relation type
C19orf33	TF binding region
C19orf33	CpG island
ENSG00000167645	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000272195	Chromatin interaction
ENSG00000006704	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000200209	Chromatin interaction
ENSG00000099338	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000267748	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000140006	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11671779	0.84[CEU][hapmap]
rs11673012	0.84[CEU][hapmap]
rs11673222	0.84[CEU][hapmap]
rs11881305	0.96[GIH][hapmap];0.97[TSI][hapmap]
rs12609247	0.85[GIH][hapmap];0.89[EUR][1000 genomes]
rs12611255	0.90[EUR][1000 genomes]
rs2270094	0.84[CEU][hapmap]
rs2270095	1.00[CEU][hapmap];0.93[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs2286475	0.92[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2286476	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs3178327	0.98[GIH][hapmap];0.97[TSI][hapmap]
rs3745951	0.84[CEU][hapmap]
rs3815345	0.84[EUR][1000 genomes]
rs3843754	0.96[GIH][hapmap];0.97[TSI][hapmap]
rs4312417	0.91[GIH][hapmap];0.97[TSI][hapmap]
rs4386247	0.84[CEU][hapmap]
rs4802324	0.90[TSI][hapmap]
rs4803999	0.81[AFR][1000 genomes]
rs4804046	0.84[CEU][hapmap]
rs56849284	0.88[EUR][1000 genomes]
rs58728151	0.86[EUR][1000 genomes]
rs59898212	0.81[EUR][1000 genomes]
rs60071299	0.86[EUR][1000 genomes]
rs61160177	0.93[EUR][1000 genomes]
rs71354995	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7252835	0.89[EUR][1000 genomes]
rs7253960	0.93[EUR][1000 genomes]
rs73043010	0.89[EUR][1000 genomes]
rs8106900	0.88[CEU][hapmap]
rs8112211	1.00[CEU][hapmap];0.96[GIH][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs931749	0.84[CEU][hapmap]
rs931750	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv960928	chr19:38790012-38822380	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2304176	SELV	cis	parietal	SCAN
rs2304176	C19orf33	cis	Heart Left Ventricle	GTEx
rs2304176	APOC4	cis	cerebellum	SCAN
rs2304176	C19orf33	cis	normal skin	skin_eQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38769400-38795200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr19:38771400-38805800	Weak transcription	Right Atrium	heart
3	chr19:38781200-38795800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr19:38781200-38805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:38781400-38795400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr19:38781400-38797800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr19:38781600-38795600	Weak transcription	Right Ventricle	heart
8	chr19:38782000-38806000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:38782400-38798000	Weak transcription	Fetal Thymus	thymus
10	chr19:38782600-38796400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr19:38783000-38795600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr19:38783400-38797000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr19:38783600-38795200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:38784000-38797200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:38784000-38805800	Weak transcription	Primary B cells from cord blood	blood
16	chr19:38785200-38795200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:38785200-38795400	Weak transcription	Primary T cells from cord blood	blood
18	chr19:38785200-38795400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:38785400-38795400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:38785400-38797000	Weak transcription	Brain Anterior Caudate	brain
21	chr19:38790000-38797800	Weak transcription	Ovary	ovary
22	chr19:38791600-38796600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:38791600-38798000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:38791800-38797000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr19:38791800-38797600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:38791800-38797800	Weak transcription	HSMMtube	muscle
27	chr19:38791800-38797800	Weak transcription	Osteobl	bone
28	chr19:38791800-38798000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:38792000-38796200	Weak transcription	Liver	Liver
30	chr19:38792000-38797600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:38792000-38805400	Weak transcription	NHDF-Ad	bronchial
32	chr19:38792000-38805800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:38792800-38795400	Weak transcription	Dnd41	blood
34	chr19:38793000-38796000	Genic enhancers	K562	blood
35	chr19:38793400-38797600	Weak transcription	Colon Smooth Muscle	Colon
36	chr19:38793800-38796000	Active TSS	A549	lung
37	chr19:38793800-38796000	Active TSS	Hela-S3	cervix
38	chr19:38794000-38796200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:38794000-38796600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
40	chr19:38794000-38796600	Transcr. at gene 5' and 3'	NHEK	skin
41	chr19:38794200-38795000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:38794200-38795200	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr19:38794200-38795200	Enhancers	Primary hematopoietic stem cells	blood
44	chr19:38794200-38795400	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr19:38794200-38795400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:38794200-38795600	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr19:38794200-38795800	Active TSS	H9 Cell Line	embryonic stem cell
48	chr19:38794200-38795800	Strong transcription	Brain Hippocampus Middle	brain
49	chr19:38794200-38795800	Active TSS	Esophagus	oesophagus
50	chr19:38794200-38796200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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