Variant report

Variant	rs1405553
Chromosome Location	chr12:41726649-41726650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10880054	0.80[JPT][hapmap]
rs1534280	0.80[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.81[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	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv832383	chr12:41693298-41846934	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1405553	PDZRN4	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41721200-41729600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:41721400-41726800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr12:41721400-41727000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:41721400-41727600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr12:41721400-41728000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:41721600-41726800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:41721600-41727000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:41721600-41727000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:41721600-41727000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:41721600-41727600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:41722800-41733000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:41723200-41731200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:41723600-41727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:41725600-41726800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr12:41726000-41728600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr12:41726200-41727200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:41726200-41727400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:41726200-41727400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:41726200-41728000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:41726400-41727800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:41726600-41727800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:41726600-41728800	Enhancers	Brain Germinal Matrix	brain

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