Variant report

Variant	rs2608717
Chromosome Location	chr12:41908987-41908988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10506195	0.80[YRI][hapmap]
rs11180971	0.83[JPT][hapmap]
rs12299762	0.85[MEX][hapmap]
rs169564	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2446145	0.82[EUR][1000 genomes]
rs2468312	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2599254	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2608698	0.82[EUR][1000 genomes]
rs2608699	0.82[EUR][1000 genomes]
rs2608713	0.83[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2730812	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs2730815	0.82[EUR][1000 genomes]
rs2730825	0.82[EUR][1000 genomes]
rs2730831	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2730832	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs2733284	0.86[JPT][hapmap]
rs2733288	0.83[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs285551	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs285552	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs285553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs285554	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs285558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs285559	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs285570	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs285571	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs285572	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs285573	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs285574	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs285576	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs285588	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs285589	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs285591	0.82[GIH][hapmap];0.82[EUR][1000 genomes]
rs285594	0.94[EUR][1000 genomes]
rs285596	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs285597	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs287087	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs389166	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs392217	0.96[EUR][1000 genomes]
rs7133340	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2608717	PDZRN4	cis	brain	seeQTL
rs2608717	KIF21A	cis	cerebellum	SCAN
rs2608717	PDZRN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41898600-41915400	Weak transcription	Aorta	Aorta
2	chr12:41902000-41909400	Enhancers	Brain Germinal Matrix	brain
3	chr12:41902400-41915000	Weak transcription	Brain Anterior Caudate	brain
4	chr12:41904600-41915600	Weak transcription	Fetal Kidney	kidney
5	chr12:41905200-41916400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:41906800-41909000	Enhancers	Fetal Brain Female	brain
7	chr12:41907200-41909000	Enhancers	Fetal Brain Male	brain
8	chr12:41907800-41915400	Weak transcription	Fetal Stomach	stomach
9	chr12:41908000-41915400	Weak transcription	Brain Hippocampus Middle	brain
10	chr12:41908000-41915800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:41908200-41915400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:41908400-41909600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:41908400-41909600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:41908600-41909400	Weak transcription	Brain Substantia Nigra	brain
15	chr12:41908600-41909800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:41908600-41910000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr12:41908600-41915400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:41908800-41910000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:41908800-41915000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:41908800-41915600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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