Variant report

Variant	rs285574
Chromosome Location	chr12:41916412-41916413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11180971	0.83[JPT][hapmap]
rs11181001	0.81[CHB][hapmap]
rs2608717	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2733284	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs285552	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs285553	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs285558	1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs285576	0.90[ASN][1000 genomes]
rs389166	0.90[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv899040	chr12:41905897-42181706	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs285574	PDZRN4	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41914000-41917200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:41914600-41917400	Enhancers	HSMM	muscle
3	chr12:41915000-41916600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr12:41915000-41916600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:41915400-41916600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr12:41915400-41917200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:41915800-41916600	Enhancers	Primary B cells from cord blood	blood
8	chr12:41915800-41916600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:41915800-41916600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:41915800-41916600	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr12:41915800-41916600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:41915800-41916600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:41915800-41916600	Flanking Active TSS	HUVEC	blood vessel
14	chr12:41916000-41916600	Enhancers	Primary hematopoietic stem cells	blood
15	chr12:41916000-41916600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr12:41916000-41921200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:41916000-41927400	Weak transcription	Aorta	Aorta
18	chr12:41916200-41916600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:41916200-41916600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:41916200-41916600	Enhancers	Brain Substantia Nigra	brain
21	chr12:41916200-41916800	Enhancers	HSMMtube	muscle
22	chr12:41916200-41922000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:41916400-41916600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:41916400-41916600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr12:41916400-41916600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:41916400-41916600	Enhancers	Adipose Nuclei	Adipose
27	chr12:41916400-41916600	Active TSS	Monocytes-CD14+_RO01746	blood
28	chr12:41916400-41916600	Flanking Active TSS	NHDF-Ad	bronchial
29	chr12:41916400-41916600	Enhancers	NHLF	lung
30	chr12:41916400-41916800	Enhancers	Dnd41	blood
31	chr12:41916400-41917400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr12:41916400-41918200	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:41916400-41921400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:41916400-41924600	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:41916400-41925200	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links