Variant report

Variant	rs1374652
Chromosome Location	chr4:30788380-30788381
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10517216	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11721555	0.87[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11723028	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11941127	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11946238	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12509289	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs13135261	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1374650	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs1374651	0.89[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374654	0.98[ASN][1000 genomes]
rs1447371	0.80[ASN][1000 genomes]
rs1550896	0.86[CEU][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16884042	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16884047	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16884163	0.80[ASN][1000 genomes]
rs1823196	0.81[JPT][hapmap]
rs1823197	0.91[JPT][hapmap]
rs1900571	0.80[ASN][1000 genomes]
rs2029202	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2121656	1.00[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs2121659	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166718	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34211313	0.80[ASN][1000 genomes]
rs34343083	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6810526	0.87[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6819990	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6820160	0.87[CEU][hapmap];0.81[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6820710	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6842641	0.90[JPT][hapmap]
rs6842866	0.80[ASN][1000 genomes]
rs6844742	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs6845219	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7664916	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7682792	0.80[ASN][1000 genomes]
rs7687637	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7700046	0.91[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs958274	0.83[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1374652	PCDH7	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:30771200-30789400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:30779200-30790600	Weak transcription	Fetal Lung	lung
3	chr4:30784600-30790600	Weak transcription	Aorta	Aorta
4	chr4:30785400-30790800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:30785600-30790200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:30785600-30790400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:30785600-30790800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:30785800-30789800	Weak transcription	Fetal Heart	heart
9	chr4:30785800-30790600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:30786000-30790600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:30786000-30790800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:30787400-30788400	Enhancers	Fetal Stomach	stomach
13	chr4:30787800-30788400	Enhancers	Ovary	ovary
14	chr4:30788000-30790600	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:30788200-30788400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:30788200-30790400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:30788200-30790800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:30788200-30791000	Weak transcription	Rectal Smooth Muscle	rectum

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