Variant report

Variant	rs2301235
Chromosome Location	chr19:41724671-41724672
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	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	CREB1	chr19:41724283-41725419	A549	lung:	n/a	n/a
4	POLR2A	chr19:41724585-41725339	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr19:41724369-41725625	HCT-116	colon:	n/a	n/a
6	POLR2A	chr19:41724470-41725433	PFSK-1	brain:	n/a	n/a
7	YY1	chr19:41724588-41725431	H1-hESC	embryonic stem cell:	n/a	chr19:41725240-41725251 chr19:41724766-41724777 chr19:41725165-41725176
8	POLR2A	chr19:41724282-41725371	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:41724465-41726897	HUVEC	blood vessel:	n/a	n/a
10	SIN3AK20	chr19:41724669-41725251	A549	lung:	n/a	n/a
11	SIN3AK20	chr19:41724490-41725453	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr19:41724631-41725410	PANC-1	pancreas:	n/a	n/a
13	POLR2A	chr19:41724466-41724992	A549	lung:	n/a	n/a
14	MAX	chr19:41724449-41725285	H1-hESC	embryonic stem cell:	n/a	n/a
15	CHD1	chr19:41723521-41728557	IMR90	lung:	n/a	n/a
16	STAT3	chr19:41724455-41725041	MCF10A-Er-Src	breast:	n/a	chr19:41724959-41724971
17	BCL3	chr19:41724260-41725333	A549	lung:	n/a	chr19:41724773-41724786 chr19:41724869-41724877
18	TEAD4	chr19:41724500-41725159	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr19:41724443-41725393	HUVEC	blood vessel:	n/a	n/a
20	MAX	chr19:41724473-41725263	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF12	chr19:41724038-41725897	A549	lung:	n/a	n/a
22	GATA3	chr19:41724181-41725521	A549	lung:	n/a	n/a
23	POLR2A	chr19:41723657-41728511	IMR90	lung:	n/a	n/a
24	POLR2A	chr19:41724403-41725407	A549	lung:	n/a	n/a
25	ATF3	chr19:41724115-41725257	A549	lung:	n/a	chr19:41724649-41724660
26	POLR2A	chr19:41724517-41725478	ProgFib	skin:	n/a	n/a
27	BACH1	chr19:41724645-41725082	H1-hESC	embryonic stem cell:	n/a	n/a
28	SIN3AK20	chr19:41724496-41725263	H1-hESC	embryonic stem cell:	n/a	n/a
29	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
30	CREB1	chr19:41724425-41725211	H1-hESC	embryonic stem cell:	n/a	n/a
31	MAZ	chr19:41724060-41728467	IMR90	lung:	n/a	chr19:41727616-41727627 chr19:41725490-41725499
32	SIN3AK20	chr19:41724231-41725331	A549	lung:	n/a	n/a
33	POLR2A	chr19:41724594-41724723	MCF-7	breast:	n/a	n/a
34	POLR2A	chr19:41724244-41726694	HUVEC	blood vessel:	n/a	n/a
35	MAX	chr19:41723526-41726982	A549	lung:	n/a	chr19:41725490-41725499 chr19:41723929-41723936
36	REST	chr19:41724361-41724810	MCF-7	breast:	n/a	chr19:41724774-41724787
37	POLR2A	chr19:41724557-41724754	H1-hESC	embryonic stem cell:	n/a	n/a
38	MYC	chr19:41724457-41725280	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr19:41724535-41725467	Gliobla	brain:	n/a	n/a
40	POLR2A	chr19:41724500-41724746	A549	lung:	n/a	n/a
41	FOXP2	chr19:41724424-41724834	PFSK-1	brain:	n/a	n/a
42	MYC	chr19:41724541-41724718	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr19:41724527-41734977	U87	brain:	n/a	n/a
44	ZBTB7A	chr19:41724597-41725492	ECC-1	luminal epithelium:	n/a	n/a
45	EP300	chr19:41724031-41725506	A549	lung:	n/a	chr19:41725137-41725153 chr19:41724870-41724886 chr19:41725414-41725430
46	MAX	chr19:41723978-41725497	A549	lung:	n/a	n/a
47	EP300	chr19:41724131-41725390	A549	lung:	n/a	chr19:41725137-41725153 chr19:41724870-41724886
48	REST	chr19:41724262-41725291	A549	lung:	n/a	chr19:41725225-41725238 chr19:41725208-41725218 chr19:41724774-41724787 chr19:41724867-41724876 chr19:41725172-41725185 chr19:41724911-41724929
49	MAX	chr19:41724472-41725386	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr19:41724420-41725344	HCT-116	colon:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:41724653-41724703	HL-60	blood:	n/a
2	chr19:41724653-41724703	NH-A	brain:	n/a
3	chr19:41724653-41724703	Hela-S3	cervix:	n/a
4	chr19:41724653-41724703	AG04449	skin:	fetal
5	chr19:41724653-41724703	Hepatocyte	liver:	n/a
6	chr19:41724653-41724703	GM12878	blood:	n/a
7	chr19:41724653-41724703	SK-N-SH_RA	brain:	n/a
8	chr19:41724653-41724703	HCPEpiC	choroid plexus:	n/a
9	chr19:41724653-41724703	GM19239	blood:	n/a
10	chr19:41724653-41724703	BJ	skin:	n/a
11	chr19:41724653-41724703	HepG2	liver:	n/a
12	chr19:41724653-41724703	NT2-D1	testis:	n/a
13	chr19:41724653-41724703	NHBE	bronchial:	n/a
14	chr19:41724653-41724703	PrEC	prostate:	n/a
15	chr19:41724653-41724703	Caco-2	colon:	n/a
16	chr19:41724653-41724703	HCT-116	colon:	n/a
17	chr19:41724653-41724703	HNPCEpiC	eye:	n/a
18	chr19:41724653-41724703	HEK293	kidney:	embryo
19	chr19:41724653-41724703	NHDF-neo	bronchial:	n/a
20	chr19:41724653-41724703	BE2_C	brain:	n/a
21	chr19:41724653-41724703	HEEpiC	esophagus:	n/a
22	chr19:41724653-41724703	K562	blood:	n/a
23	chr19:41724653-41724703	HUVEC	blood vessel:	n/a
24	chr19:41724653-41724703	HCF	heart:	n/a
25	chr19:41724653-41724703	AG10803	skin:	n/a
26	chr19:41724653-41724703	SK-N-MC	brain:	n/a
27	chr19:41724653-41724703	HCM	heart:	n/a
28	chr19:41724653-41724703	HRE	kidney:	n/a
29	chr19:41724653-41724703	HAEpiC	amniotic membrane:	n/a
30	chr19:41724653-41724703	IMR90	lung:	fetal
31	chr19:41724653-41724703	Jurkat	blood:	n/a
32	chr19:41724653-41724703	HPAEpiC	pulmonary alveolar:	n/a
33	chr19:41724653-41724703	SKMC	muscle:	n/a
34	chr19:41724653-41724703	HRPEpiC	eye:	n/a
35	chr19:41724653-41724703	H1-hESC	embryonic stem cell:	embryo
36	chr19:41724653-41724703	A549	lung:	n/a
37	chr19:41724653-41724703	ovcar-3	ovarian:	n/a
38	chr19:41724653-41724703	AG04450	lung:	fetal
39	chr19:41724653-41724703	ProgFib	skin:	n/a
40	chr19:41724653-41724703	AG09309	skin:	n/a
41	chr19:41724653-41724703	NB4	blood:	n/a
42	chr19:41724653-41724703	RPTEC	kidney:	n/a
43	chr19:41724653-41724703	MCF-7	breast:	n/a
44	chr19:41724653-41724703	HRCEpiC	kidney:	n/a
45	chr19:41724653-41724703	HIPEpiC	eye:	n/a
46	chr19:41724653-41724703	MCF10A-Er-Src	breast:	n/a
47	chr19:41724653-41724703	CMK	blood:	n/a
48	chr19:41724653-41724703	HMEC	breast:	n/a
49	chr19:41724653-41724703	GM06990	blood:	n/a
50	chr19:41724653-41724703	PANC-1	pancreas:	n/a

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

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

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12611109	0.81[EUR][1000 genomes]
rs12973802	0.81[EUR][1000 genomes]
rs2301236	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34624013	0.82[EUR][1000 genomes]
rs35056590	0.82[EUR][1000 genomes]
rs62120960	0.82[EUR][1000 genomes]
rs7252107	0.83[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

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41713200-41724800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr19:41723200-41724800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr19:41723600-41724800	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr19:41723600-41725200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:41723800-41724800	Enhancers	Placenta	Placenta
6	chr19:41723800-41725000	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr19:41724200-41724800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:41724200-41724800	Active TSS	Colonic Mucosa	Colon
9	chr19:41724200-41724800	Flanking Active TSS	A549	lung
10	chr19:41724200-41726400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr19:41724200-41726400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr19:41724200-41727200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
13	chr19:41724400-41724800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
14	chr19:41724400-41724800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:41724400-41724800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:41724400-41724800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:41724400-41724800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:41724400-41724800	Enhancers	Lung	lung
19	chr19:41724400-41724800	Flanking Active TSS	Hela-S3	cervix
20	chr19:41724400-41724800	Enhancers	HUVEC	blood vessel
21	chr19:41724400-41724800	Enhancers	NH-A	brain
22	chr19:41724400-41725000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr19:41724400-41725000	Active TSS	Primary hematopoietic stem cells	blood
24	chr19:41724400-41725200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:41724400-41725200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:41724400-41725200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
27	chr19:41724400-41725200	Enhancers	K562	blood
28	chr19:41724400-41725400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:41724400-41725400	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr19:41724400-41725800	Active TSS	Muscle Satellite Cultured Cells	--
31	chr19:41724400-41726200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:41724400-41726200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:41724400-41726200	Active TSS	Fetal Kidney	kidney
34	chr19:41724400-41726400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr19:41724400-41726400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:41724400-41726400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr19:41724400-41726400	Active TSS	Aorta	Aorta
38	chr19:41724400-41726400	Bivalent/Poised TSS	Fetal Brain Female	brain
39	chr19:41724400-41726400	Active TSS	Ovary	ovary
40	chr19:41724400-41726600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:41724400-41726600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr19:41724400-41726600	Active TSS	Left Ventricle	heart
43	chr19:41724400-41726800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr19:41724400-41727000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
45	chr19:41724400-41727000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
46	chr19:41724400-41733200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:41724600-41724800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr19:41724600-41724800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
49	chr19:41724600-41724800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
50	chr19:41724600-41724800	Bivalent/Poised TSS	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links