Variant report

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10817718	0.88[CHB][hapmap]
rs10817723	0.81[ASN][1000 genomes]
rs10982557	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs10982572	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs10982598	0.83[ASN][1000 genomes]
rs11794627	0.86[CHB][hapmap]
rs1335349	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1335350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1335353	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1414145	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1414146	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978627	0.95[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4979499	0.86[CEU][hapmap]
rs4979506	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs4979512	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62577989	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029482	0.83[ASN][1000 genomes]
rs7032660	0.87[ASN][1000 genomes]
rs7849266	1.00[ASN][1000 genomes]
rs7850000	0.88[CHB][hapmap]
rs7851185	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7865971	0.86[CHB][hapmap]
rs7866695	0.95[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][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	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv893769	chr9:117936903-117985886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7040243	C9orf80	cis	cerebellum	SCAN
rs7040243	SNX30	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117930000-117964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:117945600-117959400	Weak transcription	Fetal Kidney	kidney
3	chr9:117945800-117959600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:117947000-117954200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:117947200-117953000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr9:117947200-117954400	Weak transcription	Colon Smooth Muscle	Colon

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