Variant report

Variant	rs731245
Chromosome Location	chr13:47472266-47472267
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:47472250-47472300	A549	lung:	n/a
2	chr13:47472250-47472300	ovcar-3	ovarian:	n/a
3	chr13:47472250-47472300	AG10803	skin:	n/a
4	chr13:47472250-47472300	NHDF-neo	bronchial:	n/a
5	chr13:47472250-47472300	K562	blood:	n/a
6	chr13:47472250-47472300	IMR90	lung:	fetal
7	chr13:47472250-47472300	Hepatocyte	liver:	n/a
8	chr13:47472250-47472300	HAEpiC	amniotic membrane:	n/a
9	chr13:47472250-47472300	HNPCEpiC	eye:	n/a
10	chr13:47472250-47472300	AoSMC	blood vessel:	n/a
11	chr13:47472250-47472300	MCF10A-Er-Src	breast:	n/a
12	chr13:47472250-47472300	SK-N-SH_RA	brain:	n/a
13	chr13:47472250-47472300	Hela-S3	cervix:	n/a
14	chr13:47472250-47472300	AG04450	lung:	fetal
15	chr13:47472250-47472300	HUVEC	blood vessel:	n/a
16	chr13:47472250-47472300	HCM	heart:	n/a
17	chr13:47472250-47472300	MCF-7	breast:	n/a
18	chr13:47472250-47472300	CMK	blood:	n/a
19	chr13:47472250-47472300	Caco-2	colon:	n/a
20	chr13:47472250-47472300	PFSK-1	brain:	n/a
21	chr13:47472250-47472300	SK-N-MC	brain:	n/a
22	chr13:47472250-47472300	GM19239	blood:	n/a
23	chr13:47472250-47472300	HMEC	breast:	n/a
24	chr13:47472250-47472300	BE2_C	brain:	n/a
25	chr13:47472250-47472300	HRCEpiC	kidney:	n/a
26	chr13:47472250-47472300	HCF	heart:	n/a
27	chr13:47472250-47472300	HEEpiC	esophagus:	n/a
28	chr13:47472250-47472300	H1-hESC	embryonic stem cell:	embryo
29	chr13:47472250-47472300	GM12878	blood:	n/a
30	chr13:47472250-47472300	HL-60	blood:	n/a
31	chr13:47472250-47472300	NT2-D1	testis:	n/a
32	chr13:47472250-47472300	LNCaP	prostate:	n/a
33	chr13:47472250-47472300	HepG2	liver:	n/a
34	chr13:47472250-47472300	AG04449	skin:	fetal
35	chr13:47472250-47472300	HIPEpiC	eye:	n/a
36	chr13:47472250-47472300	Jurkat	blood:	n/a
37	chr13:47472250-47472300	HPAEpiC	pulmonary alveolar:	n/a
38	chr13:47472250-47472300	AG09309	skin:	n/a
39	chr13:47472250-47472300	GM06990	blood:	n/a
40	chr13:47472250-47472300	NHBE	bronchial:	n/a
41	chr13:47472250-47472300	HRPEpiC	eye:	n/a
42	chr13:47472250-47472300	ECC-1	luminal epithelium:	n/a
43	chr13:47472250-47472300	PrEC	prostate:	n/a
44	chr13:47472250-47472300	ProgFib	skin:	n/a
45	chr13:47472250-47472300	GM12891	blood:	n/a
46	chr13:47472250-47472300	GM12892	blood:	n/a
47	chr13:47472250-47472300	SKMC	muscle:	n/a
48	chr13:47472250-47472300	HRE	kidney:	n/a
49	chr13:47472250-47472300	HEK293	kidney:	embryo
50	chr13:47472250-47472300	NB4	blood:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:47471018..47473435-chr16:2203930..2206655,2	MCF-7	breast:

No data

Variant related genes	Relation type
HTR2A	CpG island
ENSG00000131653	Chromatin interaction
ENSG00000260260	Chromatin interaction
ENSG00000206630	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1328684	0.89[LWK][hapmap];0.84[MKK][hapmap]
rs1928040	0.81[CEU][hapmap]
rs4142900	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs4941573	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4941574	0.80[EUR][1000 genomes]
rs4941575	0.85[CEU][hapmap]
rs6311	0.85[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs6313	0.85[CEU][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6561336	0.81[CEU][hapmap]
rs732821	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316236	0.80[EUR][1000 genomes]
rs9526246	0.88[CEU][hapmap]
rs9534513	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2763019	chr13:47348229-48123447	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv3447065	chr13:47472179-47472359	Weak transcription Active TSS Enhancers	CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs731245	GTF2F2	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:47469800-47472400	Active TSS	Brain Angular Gyrus	brain
2	chr13:47471200-47472600	Enhancers	Fetal Brain Male	brain
3	chr13:47471200-47473200	Weak transcription	Pancreas	Pancrea
4	chr13:47471400-47472400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr13:47471400-47474000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr13:47471600-47472400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr13:47471600-47474000	Weak transcription	Brain Hippocampus Middle	brain
8	chr13:47471600-47477600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr13:47471600-47477600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr13:47471800-47472400	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr13:47471800-47474000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:47472000-47474000	Weak transcription	Brain Anterior Caudate	brain
13	chr13:47472200-47472400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr13:47472200-47472400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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