Variant report

Variant	rs35710536
Chromosome Location	chr19:38794368-38794369
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	ZBTB33	chr19:38794168-38796572	A549	lung:	n/a	chr19:38795334-38795344
2	FOXA2	chr19:38794084-38795080	A549	lung:	n/a	n/a
3	POLR2A	chr19:38790918-38797378	PANC-1	pancreas:	n/a	n/a
4	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
5	EP300	chr19:38794305-38796151	ECC-1	luminal epithelium:	n/a	chr19:38795382-38795398 chr19:38795409-38795422 chr19:38795147-38795163
6	POLR2A	chr19:38794268-38796429	HCT-116	colon:	n/a	n/a
7	POLR2A	chr19:38794147-38796192	K562	blood:	n/a	n/a
8	ELF1	chr19:38794160-38796209	A549	lung:	n/a	n/a
9	GABPA	chr19:38794135-38795020	A549	lung:	n/a	n/a
10	POLR2A	chr19:38794272-38794944	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr19:38794325-38796169	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr19:38794286-38796311	H1-hESC	embryonic stem cell:	n/a	n/a
13	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
14	TCF12	chr19:38793963-38796680	A549	lung:	n/a	chr19:38796391-38796399 chr19:38795248-38795255
15	NR3C1	chr19:38794333-38795161	A549	lung:	n/a	n/a
16	POLR2A	chr19:38794314-38796386	K562	blood:	n/a	n/a
17	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
18	GABPA	chr19:38794324-38795058	MCF-7	breast:	n/a	n/a
19	BHLHE40	chr19:38794338-38795860	A549	lung:	n/a	chr19:38794500-38794516 chr19:38795353-38795362 chr19:38795353-38795362 chr19:38795354-38795363
20	POLR2A	chr19:38794240-38796636	Hela-S3	cervix:	n/a	n/a
21	BRCA1	chr19:38794292-38794380	H1-hESC	embryonic stem cell:	n/a	n/a
22	CREB1	chr19:38794262-38796236	A549	lung:	n/a	n/a
23	JUND	chr19:38794302-38796622	A549	lung:	n/a	chr19:38794754-38794764 chr19:38794753-38794765 chr19:38794755-38794763
24	POLR2A	chr19:38794309-38795933	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr19:38794327-38796008	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr19:38794367-38796249	MCF-7	breast:	n/a	n/a
27	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
28	ATF3	chr19:38794088-38796300	A549	lung:	n/a	n/a
29	USF1	chr19:38794207-38796162	A549	lung:	n/a	chr19:38794500-38794516 chr19:38795353-38795362 chr19:38795353-38795362 chr19:38795354-38795363
30	REST	chr19:38794061-38796560	A549	lung:	n/a	chr19:38795685-38795695 chr19:38794570-38794583 chr19:38795654-38795667 chr19:38794832-38794845 chr19:38794829-38794842
31	BCL3	chr19:38794125-38796665	A549	lung:	n/a	chr19:38794754-38794763 chr19:38794532-38794541 chr19:38796292-38796305
32	SIN3AK20	chr19:38794180-38796051	A549	lung:	n/a	n/a
33	MAX	chr19:38794004-38796441	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
34	POLR2A	chr19:38794243-38796316	A549	lung:	n/a	n/a
35	POLR2A	chr19:38794118-38796607	HCT-116	colon:	n/a	n/a
36	YY1	chr19:38794321-38796142	A549	lung:	n/a	chr19:38795391-38795402 chr19:38795232-38795241
37	GATA3	chr19:38794042-38796511	A549	lung:	n/a	n/a
38	E2F6	chr19:38794217-38796261	A549	lung:	n/a	chr19:38795157-38795169
39	FOSL2	chr19:38794039-38796543	A549	lung:	n/a	chr19:38794754-38794764 chr19:38794753-38794765 chr19:38794755-38794763
40	POLR2A	chr19:38794248-38794530	HepG2	liver:	n/a	n/a
41	REST	chr19:38794135-38796288	A549	lung:	n/a	chr19:38795685-38795695 chr19:38794570-38794583 chr19:38795654-38795667 chr19:38794832-38794845 chr19:38794829-38794842
42	FOSL2	chr19:38794245-38795080	A549	lung:	n/a	chr19:38794754-38794764 chr19:38794753-38794765 chr19:38794755-38794763
43	POLR2A	chr19:38794303-38796273	ECC-1	luminal epithelium:	n/a	n/a
44	EP300	chr19:38794137-38796457	A549	lung:	n/a	chr19:38795382-38795398 chr19:38795409-38795422 chr19:38795147-38795163
45	POLR2A	chr19:38792895-38797330	K562	blood:	n/a	n/a
46	TCF12	chr19:38794054-38796277	A549	lung:	n/a	chr19:38795248-38795255
47	POLR2A	chr19:38794281-38796164	A549	lung:	n/a	n/a
48	ETS1	chr19:38794141-38795054	A549	lung:	n/a	chr19:38794830-38794841
49	POLR2A	chr19:38790968-38797461	PANC-1	pancreas:	n/a	n/a
50	POLR2A	chr19:38794108-38795046	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38753031..38764322-chr19:38787496..38798494,54	MCF-7	breast:
2	chr19:38793026..38794538-chr19:38866336..38868984,2	K562	blood:
3	chr19:38718266..38721870-chr19:38794040..38798765,4	MCF-7	breast:
4	chr19:38793175..38794787-chr19:38818413..38820106,2	MCF-7	breast:
5	chr19:38793982..38798570-chr19:38826004..38829304,4	K562	blood:
6	chr19:38794216..38796351-chr19:38852337..38854290,3	MCF-7	breast:
7	chr19:38793475..38795482-chr19:38826442..38828638,2	K562	blood:
8	chr19:38791989..38796796-chr19:38825093..38829391,7	MCF-7	breast:
9	chr19:38793114..38794677-chr5:14438163..14440684,2	MCF-7	breast:
10	chr19:38784964..38786694-chr19:38794356..38796889,2	K562	blood:
11	chr19:38744771..38747370-chr19:38793659..38796631,3	MCF-7	breast:

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

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11878707	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17640544	1.00[TSI][hapmap]
rs2302226	1.00[ASW][hapmap]
rs34614180	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35077481	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35323359	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3745962	1.00[ASW][hapmap]
rs3859550	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71354996	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8101482	1.00[GIH][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

No data

Chromatin state (count:108 , 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	chr19:38781000-38794400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr19:38781200-38795800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:38781200-38805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:38781400-38795400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr19:38781400-38797800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr19:38781600-38795600	Weak transcription	Right Ventricle	heart
10	chr19:38782000-38806000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:38782400-38798000	Weak transcription	Fetal Thymus	thymus
12	chr19:38782600-38796400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr19:38783000-38795600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr19:38783400-38797000	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr19:38783600-38795200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:38784000-38794600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr19:38784000-38797200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr19:38784000-38805800	Weak transcription	Primary B cells from cord blood	blood
19	chr19:38784200-38794400	Weak transcription	Thymus	Thymus
20	chr19:38784400-38794400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr19:38785200-38795200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:38785200-38795400	Weak transcription	Primary T cells from cord blood	blood
23	chr19:38785200-38795400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr19:38785400-38794400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr19:38785400-38794600	Weak transcription	Brain Substantia Nigra	brain
26	chr19:38785400-38794800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr19:38785400-38795400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:38785400-38797000	Weak transcription	Brain Anterior Caudate	brain
29	chr19:38785600-38794400	Weak transcription	Brain Angular Gyrus	brain
30	chr19:38785600-38794800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr19:38789600-38794400	Weak transcription	Aorta	Aorta
32	chr19:38790000-38797800	Weak transcription	Ovary	ovary
33	chr19:38790200-38794600	Weak transcription	Adipose Nuclei	Adipose
34	chr19:38791600-38794400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr19:38791600-38794400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr19:38791600-38794600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr19:38791600-38796600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:38791600-38798000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:38791800-38794400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr19:38791800-38794400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr19:38791800-38794400	Weak transcription	Gastric	stomach
42	chr19:38791800-38794400	Weak transcription	NH-A	brain
43	chr19:38791800-38794800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr19:38791800-38794800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:38791800-38794800	Weak transcription	Pancreas	Pancrea
46	chr19:38791800-38797000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:38791800-38797600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:38791800-38797800	Weak transcription	HSMMtube	muscle
49	chr19:38791800-38797800	Weak transcription	Osteobl	bone
50	chr19:38791800-38798000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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