Variant report

Variant	rs1463847
Chromosome Location	chr4:31149725-31149726
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10013484	0.84[EUR][1000 genomes]
rs10028386	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs10030161	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1044352	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044353	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937565	1.00[YRI][hapmap]
rs1463845	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1463846	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1463848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463849	0.85[EUR][1000 genomes]
rs1499476	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs16867994	0.93[LWK][hapmap];1.00[YRI][hapmap]
rs16867997	0.93[LWK][hapmap];1.00[YRI][hapmap]
rs16884382	1.00[YRI][hapmap]
rs16884451	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884471	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884473	0.85[EUR][1000 genomes]
rs1827140	0.81[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs1827141	0.88[CEU][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs1846526	0.90[EUR][1000 genomes]
rs28483036	0.85[EUR][1000 genomes]
rs28498976	0.85[EUR][1000 genomes]
rs3733655	0.88[AFR][1000 genomes]
rs3857021	0.88[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4692500	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448743	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6448744	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6818974	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6820584	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs6834969	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs7655744	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7671046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674487	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs7686226	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7693529	0.86[EUR][1000 genomes]
rs952617	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9996642	0.85[EUR][1000 genomes]

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	nsv998450	chr4:30823631-31628179	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1007884	chr4:31071934-31680623	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1007145	chr4:31079681-31670541	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv491749	chr4:31103307-31645668	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1463847	PCDH7	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:31142600-31150000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:31143000-31150400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:31143000-31151800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:31145600-31154400	Weak transcription	Fetal Heart	heart
5	chr4:31146600-31150400	Weak transcription	Fetal Lung	lung
6	chr4:31147000-31150400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:31147800-31150600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:31148400-31150400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:31148400-31150400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:31148600-31150800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:31149000-31150200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:31149200-31151800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr4:31149400-31150600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr4:31149400-31151400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr4:31149600-31151600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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