Variant report

Variant	rs2301236
Chromosome Location	chr19:41724820-41724821
allele	A/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	POLR2A	chr19:41724565-41725487	Hela-S3	cervix:	n/a	n/a
2	REST	chr19:41723853-41725457	A549	lung:	n/a	chr19:41725225-41725238 chr19:41725208-41725218 chr19:41724774-41724787 chr19:41724867-41724876 chr19:41725172-41725185 chr19:41724911-41724929
3	POLR2A	chr19:41724812-41726616	U87	brain:	n/a	n/a
4	CREB1	chr19:41724283-41725419	A549	lung:	n/a	n/a
5	POLR2A	chr19:41724585-41725339	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr19:41724369-41725625	HCT-116	colon:	n/a	n/a
7	POLR2A	chr19:41724470-41725433	PFSK-1	brain:	n/a	n/a
8	ZBTB7A	chr19:41724691-41725145	K562	blood:	n/a	n/a
9	ATF2	chr19:41724760-41725261	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr19:41724588-41725431	H1-hESC	embryonic stem cell:	n/a	chr19:41725240-41725251 chr19:41724766-41724777 chr19:41725165-41725176
11	POLR2A	chr19:41724282-41725371	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:41724465-41726897	HUVEC	blood vessel:	n/a	n/a
13	SIN3AK20	chr19:41724669-41725251	A549	lung:	n/a	n/a
14	POLR2A	chr19:41724673-41725390	Hela-S3	cervix:	n/a	n/a
15	SIN3AK20	chr19:41724490-41725453	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr19:41724631-41725410	PANC-1	pancreas:	n/a	n/a
17	SIN3AK20	chr19:41724796-41725219	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr19:41724466-41724992	A549	lung:	n/a	n/a
19	MAX	chr19:41724449-41725285	H1-hESC	embryonic stem cell:	n/a	n/a
20	CHD1	chr19:41723521-41728557	IMR90	lung:	n/a	n/a
21	STAT3	chr19:41724455-41725041	MCF10A-Er-Src	breast:	n/a	chr19:41724959-41724971
22	BCL3	chr19:41724260-41725333	A549	lung:	n/a	chr19:41724773-41724786 chr19:41724869-41724877
23	TEAD4	chr19:41724500-41725159	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:41724443-41725393	HUVEC	blood vessel:	n/a	n/a
25	MAX	chr19:41724473-41725263	H1-hESC	embryonic stem cell:	n/a	n/a
26	ATF2	chr19:41724745-41725219	H1-hESC	embryonic stem cell:	n/a	n/a
27	TCF12	chr19:41724038-41725897	A549	lung:	n/a	n/a
28	GATA3	chr19:41724181-41725521	A549	lung:	n/a	n/a
29	POLR2A	chr19:41723657-41728511	IMR90	lung:	n/a	n/a
30	POLR2A	chr19:41724403-41725407	A549	lung:	n/a	n/a
31	CHD2	chr19:41724817-41725185	H1-hESC	embryonic stem cell:	n/a	n/a
32	RAD21	chr19:41724767-41725208	H1-hESC	embryonic stem cell:	n/a	n/a
33	SP4	chr19:41724800-41725250	H1-hESC	embryonic stem cell:	n/a	n/a
34	ATF3	chr19:41724115-41725257	A549	lung:	n/a	chr19:41724649-41724660
35	POLR2A	chr19:41724517-41725478	ProgFib	skin:	n/a	n/a
36	BACH1	chr19:41724645-41725082	H1-hESC	embryonic stem cell:	n/a	n/a
37	SIN3AK20	chr19:41724496-41725263	H1-hESC	embryonic stem cell:	n/a	n/a
38	SP1	chr19:41724141-41726706	A549	lung:	n/a	chr19:41726252-41726266 chr19:41724786-41724800 chr19:41724939-41724953 chr19:41725241-41725253 chr19:41724968-41724975 chr19:41725247-41725259 chr19:41724784-41724793 chr19:41726382-41726396 chr19:41725249-41725258 chr19:41725242-41725256 chr19:41725437-41725451 chr19:41725109-41725123 chr19:41725047-41725059 chr19:41724779-41724793 chr19:41724773-41724787 chr19:41725403-41725412 chr19:41724783-41724792 chr19:41725247-41725259
39	CREB1	chr19:41724425-41725211	H1-hESC	embryonic stem cell:	n/a	n/a
40	TAF1	chr19:41724797-41725144	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr19:41724060-41728467	IMR90	lung:	n/a	chr19:41727616-41727627 chr19:41725490-41725499
42	SIN3AK20	chr19:41724231-41725331	A549	lung:	n/a	n/a
43	EGR1	chr19:41724763-41725290	H1-hESC	embryonic stem cell:	n/a	chr19:41725244-41725257 chr19:41724778-41724791
44	USF1	chr19:41724799-41725115	H1-hESC	embryonic stem cell:	n/a	chr19:41725063-41725079
45	POLR2A	chr19:41724757-41724976	A549	lung:	n/a	n/a
46	POLR2A	chr19:41724244-41726694	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr19:41724751-41726627	HUVEC	blood vessel:	n/a	n/a
48	MAX	chr19:41723526-41726982	A549	lung:	n/a	chr19:41725490-41725499 chr19:41723929-41723936
49	MAX	chr19:41724816-41725117	H1-hESC	embryonic stem cell:	n/a	n/a
50	TAF1	chr19:41724773-41725186	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:64194232..64194886-chr19:41724694..41725687,2	Hela-S3	cervix:
2	chr19:41723294..41725372-chr19:41769177..41770875,2	MCF-7	breast:
3	chr19:41723453..41725082-chr19:41766152..41768338,2	MCF-7	breast:
4	chr11:67797865..67798398-chr19:41724615..41725298,2	Hela-S3	cervix:

Variant related genes	Relation type
AXL	TF binding region
ENSG00000255306	Chromatin interaction
ENSG00000126821	Chromatin interaction
ENSG00000110717	Chromatin interaction
ENSG00000105323	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12611109	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12611144	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12973802	0.83[EUR][1000 genomes]
rs1709106	0.81[YRI][hapmap]
rs2301235	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34624013	0.84[EUR][1000 genomes]
rs35056590	0.84[EUR][1000 genomes]
rs62120960	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7252107	0.80[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911768	chr19:41680424-41748753	Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2301236	QPCTL	cis	parietal	SCAN
rs2301236	SYMPK	cis	parietal	SCAN
rs2301236	EML2	cis	cerebellum	SCAN
rs2301236	MARK4	cis	parietal	SCAN
rs2301236	RTN2	cis	parietal	SCAN
rs2301236	HRC	cis	parietal	SCAN
rs2301236	PSG9	cis	parietal	SCAN
rs2301236	AP2A1	cis	cerebellum	SCAN
rs2301236	SEC1	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41723600-41725200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:41723800-41725000	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr19:41724200-41726400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr19:41724200-41726400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr19:41724200-41727200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
6	chr19:41724400-41725000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:41724400-41725000	Active TSS	Primary hematopoietic stem cells	blood
8	chr19:41724400-41725200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:41724400-41725200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:41724400-41725200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
11	chr19:41724400-41725200	Enhancers	K562	blood
12	chr19:41724400-41725400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:41724400-41725400	Flanking Active TSS	Brain Germinal Matrix	brain
14	chr19:41724400-41725800	Active TSS	Muscle Satellite Cultured Cells	--
15	chr19:41724400-41726200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:41724400-41726200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:41724400-41726200	Active TSS	Fetal Kidney	kidney
18	chr19:41724400-41726400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr19:41724400-41726400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:41724400-41726400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:41724400-41726400	Active TSS	Aorta	Aorta
22	chr19:41724400-41726400	Bivalent/Poised TSS	Fetal Brain Female	brain
23	chr19:41724400-41726400	Active TSS	Ovary	ovary
24	chr19:41724400-41726600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:41724400-41726600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr19:41724400-41726600	Active TSS	Left Ventricle	heart
27	chr19:41724400-41726800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
28	chr19:41724400-41727000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
29	chr19:41724400-41727000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
30	chr19:41724400-41733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr19:41724600-41725000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr19:41724600-41725000	Weak transcription	Gastric	stomach
33	chr19:41724600-41725000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
34	chr19:41724600-41725400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:41724600-41725400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
36	chr19:41724600-41725600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:41724600-41725800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:41724600-41725800	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr19:41724600-41725800	Bivalent Enhancer	Fetal Brain Male	brain
40	chr19:41724600-41725800	Active TSS	Fetal Lung	lung
41	chr19:41724600-41725800	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr19:41724600-41726200	Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr19:41724600-41726200	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr19:41724600-41726200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:41724600-41726200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:41724600-41726200	Active TSS	Esophagus	oesophagus
47	chr19:41724600-41726200	Bivalent/Poised TSS	Fetal Stomach	stomach
48	chr19:41724600-41726200	Active TSS	Placenta Amnion	Placenta Amnion
49	chr19:41724600-41726200	Active TSS	NHEK	skin
50	chr19:41724600-41726400	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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