Variant report

Variant	rs2710263
Chromosome Location	chr12:41902353-41902354
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:122)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:41902312-41902362	AG04449	skin:	fetal
2	chr12:41902309-41902359	BE2_C	brain:	n/a
3	chr12:41902309-41902359	GM06990	blood:	n/a
4	chr12:41902312-41902362	Jurkat	blood:	n/a
5	chr12:41902312-41902362	SK-N-SH	brain:	n/a
6	chr12:41902309-41902359	T-47D	breast:	n/a
7	chr12:41902312-41902362	HPAEpiC	pulmonary alveolar:	n/a
8	chr12:41902309-41902359	PFSK-1	brain:	n/a
9	chr12:41902312-41902362	IMR90	lung:	fetal
10	chr12:41902312-41902362	LNCaP	prostate:	n/a
11	chr12:41902312-41902362	PANC-1	pancreas:	n/a
12	chr12:41902309-41902359	BJ	skin:	n/a
13	chr12:41902312-41902362	NB4	blood:	n/a
14	chr12:41902309-41902359	HL-60	blood:	n/a
15	chr12:41902309-41902359	SAEC	small airway:	n/a
16	chr12:41902309-41902359	LNCaP	prostate:	n/a
17	chr12:41902312-41902362	NHDF-neo	bronchial:	n/a
18	chr12:41902309-41902359	AoSMC	blood vessel:	n/a
19	chr12:41902309-41902359	HPAEpiC	pulmonary alveolar:	n/a
20	chr12:41902312-41902362	HIPEpiC	eye:	n/a
21	chr12:41902312-41902362	HCM	heart:	n/a
22	chr12:41902309-41902359	HIPEpiC	eye:	n/a
23	chr12:41902312-41902362	PFSK-1	brain:	n/a
24	chr12:41902312-41902362	T-47D	breast:	n/a
25	chr12:41902309-41902359	SK-N-SH_RA	brain:	n/a
26	chr12:41902312-41902362	SAEC	small airway:	n/a
27	chr12:41902309-41902359	NHBE	bronchial:	n/a
28	chr12:41902309-41902359	K562	blood:	n/a
29	chr12:41902312-41902362	ovcar-3	ovarian:	n/a
30	chr12:41902312-41902362	HepG2	liver:	n/a
31	chr12:41902309-41902359	A549	lung:	n/a
32	chr12:41902312-41902362	GM12878	blood:	n/a
33	chr12:41902312-41902362	AG04450	lung:	fetal
34	chr12:41902312-41902362	RPTEC	kidney:	n/a
35	chr12:41902312-41902362	HCT-116	colon:	n/a
36	chr12:41902309-41902359	NB4	blood:	n/a
37	chr12:41902309-41902359	HRCEpiC	kidney:	n/a
38	chr12:41902309-41902359	HMEC	breast:	n/a
39	chr12:41902309-41902359	Caco-2	colon:	n/a
40	chr12:41902312-41902362	SK-N-SH_RA	brain:	n/a
41	chr12:41902312-41902362	HUVEC	blood vessel:	n/a
42	chr12:41902312-41902362	H1-hESC	embryonic stem cell:	embryo
43	chr12:41902312-41902362	HAEpiC	amniotic membrane:	n/a
44	chr12:41902312-41902362	AG09319	gingival:	n/a
45	chr12:41902309-41902359	HEEpiC	esophagus:	n/a
46	chr12:41902309-41902359	NHDF-neo	bronchial:	n/a
47	chr12:41902309-41902359	ECC-1	luminal epithelium:	n/a
48	chr12:41902309-41902359	GM12892	blood:	n/a
49	chr12:41902309-41902359	Hela-S3	cervix:	n/a
50	chr12:41902312-41902362	HRE	kidney:	n/a

No data

Variant related genes	Relation type
PDZRN4	CpG island

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10506195	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11615166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12811069	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12822018	0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12823312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1379779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1458170	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17129378	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs17129392	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17129427	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17578886	1.00[JPT][hapmap]
rs17768388	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1902905	0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2468313	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2710265	0.92[EUR][1000 genomes]
rs285557	0.88[EUR][1000 genomes]
rs34298736	0.89[ASN][1000 genomes]
rs34607783	0.89[ASN][1000 genomes]
rs35032376	0.89[ASN][1000 genomes]
rs35667109	0.89[ASN][1000 genomes]
rs35753665	0.89[ASN][1000 genomes]
rs57639356	0.87[ASN][1000 genomes]
rs58667777	0.89[ASN][1000 genomes]
rs7957589	1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832384	chr12:41772648-41971430	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3337301	chr12:41851654-42093677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv826349	chr12:41878846-41911495	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2710263	PDZRN4	cis	parietal	SCAN
rs2710263	ABCD2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41869600-41905200	Weak transcription	Colon Smooth Muscle	Colon
2	chr12:41877400-41903600	Weak transcription	Ovary	ovary
3	chr12:41898600-41915400	Weak transcription	Aorta	Aorta
4	chr12:41899000-41906000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:41900200-41902400	Strong transcription	Stomach Smooth Muscle	stomach
6	chr12:41900600-41903800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:41900600-41904000	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr12:41901400-41902600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:41901400-41902600	Enhancers	Brain Substantia Nigra	brain
10	chr12:41902000-41902400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr12:41902000-41902400	Enhancers	Brain Anterior Caudate	brain
12	chr12:41902000-41902600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr12:41902000-41902600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr12:41902000-41902600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:41902000-41902600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr12:41902000-41903600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr12:41902000-41909400	Enhancers	Brain Germinal Matrix	brain
18	chr12:41902200-41902600	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr12:41902200-41903400	Enhancers	Brain Hippocampus Middle	brain
20	chr12:41902200-41908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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