Variant report

Variant	rs12509904
Chromosome Location	chr4:86635567-86635568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10017047	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10033273	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1014642	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11097071	0.81[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs11735639	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11945319	0.83[GIH][hapmap];0.88[MEX][hapmap]
rs12505724	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12506038	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12507198	0.81[ASN][1000 genomes]
rs12507272	0.85[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12510148	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12510813	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12513384	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs13102863	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13106553	0.80[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13108523	0.90[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13110485	0.83[ASN][1000 genomes]
rs13110928	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13121597	0.83[ASN][1000 genomes]
rs13127367	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13128115	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs13134382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13135703	0.83[ASN][1000 genomes]
rs13136153	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13137575	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13139248	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13146939	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs13147689	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13152150	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs17010632	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs17010857	0.84[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs1871864	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs1871865	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs1966862	0.81[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap]
rs2004613	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs34056429	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34322771	0.81[ASN][1000 genomes]
rs34820504	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35250811	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35341700	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35472747	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35577842	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3889735	0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4413396	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4693731	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693734	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4693735	0.86[CHB][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4693736	0.81[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs58146546	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6531854	0.86[JPT][hapmap]
rs6813860	0.80[ASW][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs71599423	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72974953	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7439720	0.86[JPT][hapmap]
rs7676486	1.00[ASW][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7677064	0.85[JPT][hapmap]
rs900204	0.90[ASW][hapmap];0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs931195	0.86[JPT][hapmap]
rs9998523	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv829999	chr4:86500257-86666019	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12509904	ARHGAP24	cis	cerebellum	SCAN
rs12509904	PTPN13	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86625400-86638200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:86629400-86635800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr4:86629800-86635800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr4:86629800-86636200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:86629800-86636600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:86629800-86638000	Weak transcription	Fetal Lung	lung
7	chr4:86629800-86638000	Weak transcription	HSMMtube	muscle
8	chr4:86632000-86647000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr4:86633600-86644800	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:86634000-86636400	Enhancers	Primary B cells from peripheral blood	blood
11	chr4:86634200-86636800	Enhancers	Primary B cells from cord blood	blood
12	chr4:86635200-86636200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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