Variant report

Variant	rs6988046
Chromosome Location	chr8:9948433-9948434
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10098474	0.91[CHB][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs10104911	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs11990610	0.82[CHB][hapmap]
rs11990614	0.82[CHB][hapmap]
rs11998591	0.83[GIH][hapmap]
rs13261836	0.83[CHB][hapmap]
rs1484638	0.83[EUR][1000 genomes]
rs17149332	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs17151108	0.82[CHB][hapmap];0.88[GIH][hapmap];0.97[MKK][hapmap]
rs17151140	0.82[CHB][hapmap]
rs17151145	0.82[CHB][hapmap];0.88[GIH][hapmap]
rs17151147	0.82[CHB][hapmap];0.88[GIH][hapmap]
rs17151188	0.82[CHB][hapmap]
rs17151193	0.82[CHB][hapmap];0.88[GIH][hapmap]
rs1994223	0.89[CEU][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.91[TSI][hapmap]
rs1994224	0.83[CEU][hapmap];0.86[CHB][hapmap]
rs2046398	0.84[CEU][hapmap];0.86[CHB][hapmap];0.83[EUR][1000 genomes]
rs4840461	0.84[CEU][hapmap];0.90[MEX][hapmap]
rs4840463	0.82[CHB][hapmap]
rs4840464	0.87[CHB][hapmap]
rs4841280	0.94[CEU][hapmap];0.86[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7012221	0.81[ASN][1000 genomes]
rs7832431	0.82[ASN][1000 genomes]
rs7843906	0.86[CHB][hapmap];0.88[GIH][hapmap]
rs814421	1.00[ASW][hapmap];0.91[CHB][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs814422	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs814424	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs814427	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs860068	0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9329214	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs936749	0.86[CHB][hapmap]
rs963593	0.85[CHB][hapmap]

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	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1034343	chr8:9948342-10014155	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6988046	CTSB	cis	cerebellum	SCAN
rs6988046	DEFB134	cis	cerebellum	SCAN
rs6988046	MFHAS1	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9940000-9949400	Weak transcription	Spleen	Spleen
2	chr8:9940200-9948600	Weak transcription	Primary T cells from cord blood	blood
3	chr8:9945200-9950000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr8:9947200-9948600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr8:9947800-9948600	Enhancers	Osteobl	bone
6	chr8:9947800-9949800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:9948000-9951400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:9948200-9948600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr8:9948200-9952800	Weak transcription	NHDF-Ad	bronchial

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