Variant report

Variant	rs6988087
Chromosome Location	chr8:99730651-99730652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10447977	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs10755896	0.82[JPT][hapmap];0.82[TSI][hapmap]
rs10755897	0.86[TSI][hapmap]
rs10955186	0.83[TSI][hapmap]
rs10955187	0.83[TSI][hapmap]
rs10955190	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11774463	1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11778767	0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11780500	0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs11785245	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12114834	0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs12547297	1.00[JPT][hapmap];0.86[TSI][hapmap]
rs12549803	0.90[JPT][hapmap];0.86[TSI][hapmap]
rs12550783	0.82[JPT][hapmap];0.86[TSI][hapmap]
rs12677183	0.93[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs12679734	0.86[TSI][hapmap]
rs12680195	1.00[JPT][hapmap];0.84[TSI][hapmap]
rs13269932	0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs13275915	0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs2515214	0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs2515216	0.88[GIH][hapmap];0.93[TSI][hapmap]
rs2922066	0.84[TSI][hapmap]
rs2922078	0.85[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs2922082	0.85[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs34114299	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs34366206	0.95[JPT][hapmap]
rs35798019	0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs4131873	1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs4255105	0.86[TSI][hapmap]
rs4279561	1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs4292660	0.80[CEU][hapmap];0.80[CHB][hapmap];0.96[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4509292	0.82[JPT][hapmap]
rs4517094	0.86[JPT][hapmap]
rs4549741	1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs4562286	0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs4734410	0.93[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs4734414	0.90[ASN][1000 genomes]
rs4735568	0.86[TSI][hapmap]
rs4735569	0.82[JPT][hapmap]
rs4735570	0.81[TSI][hapmap]
rs4735574	0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs56126163	0.82[EUR][1000 genomes]
rs58679407	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58993030	0.94[EUR][1000 genomes]
rs6651182	0.82[JPT][hapmap];0.82[TSI][hapmap]
rs6992925	0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs7818828	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7827435	0.80[CEU][hapmap];0.80[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7838239	1.00[JPT][hapmap]
rs7845271	0.83[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9656842	0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891218	chr8:99507313-99906221	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1027025	chr8:99672977-100115315	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv539690	chr8:99672977-100115315	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv891220	chr8:99681858-99867419	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	nsv1025685	chr8:99706280-99826236	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv539691	chr8:99706280-99826236	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1031089	chr8:99715785-100399935	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6988087	NCALD	cis	cerebellum	SCAN
rs6988087	RGS22	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99676200-99738200	Weak transcription	Fetal Kidney	kidney
2	chr8:99683600-99738000	Weak transcription	NHEK	skin
3	chr8:99713200-99737600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr8:99723000-99738000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr8:99723200-99736400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr8:99723200-99736400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr8:99723200-99738000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:99723200-99738000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr8:99723200-99738200	Weak transcription	Lung	lung
10	chr8:99727400-99737400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr8:99728200-99757200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr8:99729200-99737000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr8:99729200-99738000	Weak transcription	Primary monocytes fromperipheralblood	blood

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