Variant report

Variant	rs2608713
Chromosome Location	chr12:41903298-41903299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:41903087-41903913	ECC-1	luminal epithelium:	n/a	chr12:41903196-41903209
2	NFIC	chr12:41903024-41903954	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr12:41902920-41904114	ECC-1	luminal epithelium:	n/a	n/a
4	EP300	chr12:41902954-41903947	ECC-1	luminal epithelium:	n/a	chr12:41903194-41903208
5	TCF12	chr12:41902981-41904054	ECC-1	luminal epithelium:	n/a	n/a
6	ESR1	chr12:41903163-41903842	ECC-1	luminal epithelium:	n/a	n/a
7	EGR1	chr12:41903098-41903419	ECC-1	luminal epithelium:	n/a	chr12:41903266-41903277 chr12:41903266-41903276 chr12:41903266-41903277
8	FOXM1	chr12:41902824-41904199	ECC-1	luminal epithelium:	n/a	n/a
9	EGR1	chr12:41903002-41903816	ECC-1	luminal epithelium:	n/a	chr12:41903266-41903277 chr12:41903266-41903276 chr12:41903266-41903277
10	FOXM1	chr12:41903002-41904113	ECC-1	luminal epithelium:	n/a	n/a
11	TEAD4	chr12:41902936-41904014	ECC-1	luminal epithelium:	n/a	n/a
12	RAD21	chr12:41903103-41903910	ECC-1	luminal epithelium:	n/a	n/a
13	TEAD4	chr12:41903036-41904014	ECC-1	luminal epithelium:	n/a	n/a
14	NFIC	chr12:41902941-41904071	ECC-1	luminal epithelium:	n/a	n/a
15	CEBPB	chr12:41903094-41903932	ECC-1	luminal epithelium:	n/a	chr12:41903196-41903209
16	MAX	chr12:41903053-41903988	ECC-1	luminal epithelium:	n/a	n/a
17	NR3C1	chr12:41903037-41903924	ECC-1	luminal epithelium:	n/a	n/a
18	EP300	chr12:41902904-41904133	ECC-1	luminal epithelium:	n/a	chr12:41903959-41903973 chr12:41903194-41903208
19	ESR1	chr12:41903077-41903868	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
PDZRN4	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10880077	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12298084	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299762	0.94[GIH][hapmap];0.81[TSI][hapmap];0.93[EUR][1000 genomes]
rs12313532	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12314473	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322329	0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12423463	0.82[CEU][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs12424813	1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs12817240	1.00[ASN][1000 genomes]
rs12826427	1.00[ASN][1000 genomes]
rs12826692	1.00[ASN][1000 genomes]
rs12828934	1.00[ASN][1000 genomes]
rs169564	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2254521	1.00[ASW][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446145	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468312	0.83[EUR][1000 genomes]
rs2599254	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2608698	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608699	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2608717	0.83[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2730812	0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2730815	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730825	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730831	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2730832	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2733288	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285551	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs285552	0.82[EUR][1000 genomes]
rs285553	0.82[EUR][1000 genomes]
rs285554	0.83[EUR][1000 genomes]
rs285558	0.82[EUR][1000 genomes]
rs285559	0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs285570	0.83[EUR][1000 genomes]
rs285571	0.88[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs285572	0.83[EUR][1000 genomes]
rs285573	0.83[EUR][1000 genomes]
rs285588	0.83[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs285594	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs285596	0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs285597	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs287087	0.88[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34753427	1.00[ASN][1000 genomes]
rs35366617	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35487549	1.00[ASN][1000 genomes]
rs392217	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7133340	0.94[GIH][hapmap];0.89[TSI][hapmap];0.93[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2608713	PDZRN4	cis	parietal	SCAN

Chromatin state (count:17 , 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	chr12:41900600-41903800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:41900600-41904000	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:41902000-41903600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:41902000-41909400	Enhancers	Brain Germinal Matrix	brain
9	chr12:41902200-41903400	Enhancers	Brain Hippocampus Middle	brain
10	chr12:41902200-41908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:41902400-41907400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:41902400-41907800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:41902400-41915000	Weak transcription	Brain Anterior Caudate	brain
14	chr12:41902600-41907600	Weak transcription	Brain Substantia Nigra	brain
15	chr12:41902600-41907800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:41902600-41907800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:41903200-41903800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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