Variant report

Variant	rs11140750
Chromosome Location	chr9:72488471-72488472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11140716	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11140836	1.00[CHD][hapmap]
rs11140842	1.00[CHD][hapmap]
rs12378305	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap]
rs12379253	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13283032	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284442	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13295978	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2871283	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34702508	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35822389	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022971	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7027129	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7038189	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7469302	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs766002	0.94[CEU][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7852049	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050920	chr9:72345297-72579301	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv831611	chr9:72361905-72512134	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv831612	chr9:72473778-72634253	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv471310	chr9:72479046-72508302	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv614580	chr9:72479046-72508302	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv466416	chr9:72479046-72513240	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv614581	chr9:72479046-72513240	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11140750	C9orf135	cis	parietal	SCAN
rs11140750	PTAR1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72475400-72495200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:72476200-72492800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr9:72486800-72488800	Weak transcription	NHDF-Ad	bronchial
4	chr9:72487000-72488600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:72487400-72490000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:72487600-72489200	Enhancers	Psoas Muscle	Psoas
7	chr9:72487600-72489600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr9:72487800-72490600	Enhancers	Fetal Heart	heart
9	chr9:72488000-72488600	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr9:72488200-72488800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:72488200-72492400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr9:72488400-72489000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:72488400-72489000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:72488400-72489400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr9:72488400-72492600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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