Variant report

Variant	rs35308902
Chromosome Location	chr19:38794749-38794750
allele	-/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	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	USF1	chr19:38794497-38794880	A549	lung:	n/a	chr19:38794500-38794516
49	TEAD4	chr19:38794595-38794997	H1-hESC	embryonic stem cell:	n/a	n/a
50	ATF3	chr19:38794088-38796300	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38753031..38764322-chr19:38787496..38798494,54	MCF-7	breast:
2	chr19:38718266..38721870-chr19:38794040..38798765,4	MCF-7	breast:
3	chr19:38793175..38794787-chr19:38818413..38820106,2	MCF-7	breast:
4	chr19:38779327..38783351-chr19:38794485..38798006,3	K562	blood:
5	chr19:38794669..38796308-chr19:38799482..38801247,2	K562	blood:
6	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
7	chr19:38794216..38796351-chr19:38852337..38854290,3	MCF-7	breast:
8	chr14:64108540..64109428-chr19:38794685..38795598,2	Hela-S3	cervix:
9	chr19:38794641..38795623-chr7:73867369..73868176,2	Hela-S3	cervix:
10	chr19:38793475..38795482-chr19:38826442..38828638,2	K562	blood:
11	chr19:38791989..38796796-chr19:38825093..38829391,7	MCF-7	breast:
12	chr19:38784964..38786694-chr19:38794356..38796889,2	K562	blood:
13	chr19:38744771..38747370-chr19:38793659..38796631,3	MCF-7	breast:

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

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11666449	0.87[EUR][1000 genomes]
rs11668355	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11668651	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11669131	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11669230	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11671779	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11672219	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672531	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11673012	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11673203	0.81[EUR][1000 genomes]
rs11673222	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2286473	0.87[EUR][1000 genomes]
rs2302182	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2302183	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304177	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2368484	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2887262	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34989303	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3745951	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3745952	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4386247	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs45437199	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4801723	0.81[EUR][1000 genomes]
rs4802326	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802327	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4804016	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57681346	0.88[EUR][1000 genomes]
rs60082376	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60487067	0.85[EUR][1000 genomes]
rs61091932	0.89[EUR][1000 genomes]
rs7256575	0.89[EUR][1000 genomes]
rs73041302	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs8101488	0.80[AMR][1000 genomes]
rs8104823	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8106900	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs870218	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs931749	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs931750	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]

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

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38765800-38794800	Weak transcription	Small Intestine	intestine
2	chr19:38769400-38795200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38771400-38805800	Weak transcription	Right Atrium	heart
4	chr19:38781200-38795800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr19:38781200-38805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:38781400-38795400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:38781400-38797800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr19:38781600-38795600	Weak transcription	Right Ventricle	heart
9	chr19:38782000-38806000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:38782400-38798000	Weak transcription	Fetal Thymus	thymus
11	chr19:38782600-38796400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr19:38783000-38795600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:38783400-38797000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr19:38783600-38795200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:38784000-38797200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr19:38784000-38805800	Weak transcription	Primary B cells from cord blood	blood
17	chr19:38785200-38795200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:38785200-38795400	Weak transcription	Primary T cells from cord blood	blood
19	chr19:38785200-38795400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:38785400-38794800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:38785400-38795400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr19:38785400-38797000	Weak transcription	Brain Anterior Caudate	brain
23	chr19:38785600-38794800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:38790000-38797800	Weak transcription	Ovary	ovary
25	chr19:38791600-38796600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:38791600-38798000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:38791800-38794800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:38791800-38794800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:38791800-38794800	Weak transcription	Pancreas	Pancrea
30	chr19:38791800-38797000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:38791800-38797600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr19:38791800-38797800	Weak transcription	HSMMtube	muscle
33	chr19:38791800-38797800	Weak transcription	Osteobl	bone
34	chr19:38791800-38798000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:38792000-38796200	Weak transcription	Liver	Liver
36	chr19:38792000-38797600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:38792000-38805400	Weak transcription	NHDF-Ad	bronchial
38	chr19:38792000-38805800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr19:38792800-38795400	Weak transcription	Dnd41	blood
40	chr19:38793000-38796000	Genic enhancers	K562	blood
41	chr19:38793400-38797600	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:38793800-38796000	Active TSS	A549	lung
43	chr19:38793800-38796000	Active TSS	Hela-S3	cervix
44	chr19:38794000-38794800	Flanking Active TSS	HMEC	breast
45	chr19:38794000-38796200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr19:38794000-38796600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
47	chr19:38794000-38796600	Transcr. at gene 5' and 3'	NHEK	skin
48	chr19:38794200-38794800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr19:38794200-38794800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:38794200-38795000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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