Variant report

Variant	rs10987747
Chromosome Location	chr9:101562859-101562860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr9:101562550-101562877	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101557168..101559112-chr9:101562490..101564564,2	K562	blood:
2	chr9:101557502..101560648-chr9:101561761..101566050,6	MCF-7	breast:

Variant related genes	Relation type
ANKS6	TF binding region
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10121153	0.88[EUR][1000 genomes]
rs1022796	0.84[EUR][1000 genomes]
rs10760494	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs10819308	0.89[ASW][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs10819320	0.89[ASW][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs10987749	0.91[EUR][1000 genomes]
rs10987771	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10987794	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11791440	0.84[EUR][1000 genomes]
rs12056975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12380570	0.93[ASN][1000 genomes]
rs1543506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555519	0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs168083	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs173066	0.86[ASN][1000 genomes]
rs186809	0.92[ASN][1000 genomes]
rs2146255	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337569	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs337572	0.86[ASN][1000 genomes]
rs337577	0.86[ASN][1000 genomes]
rs337578	0.86[ASN][1000 genomes]
rs337581	0.86[ASN][1000 genomes]
rs337591	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs33998698	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3889747	0.86[ASN][1000 genomes]
rs3933477	0.83[EUR][1000 genomes]
rs404680	0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs420158	0.95[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs422531	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs450231	0.92[ASN][1000 genomes]
rs4742745	0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs4743278	0.81[EUR][1000 genomes]
rs4743281	0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs532824	0.86[ASN][1000 genomes]
rs554730	0.95[ASN][1000 genomes]
rs580809	0.82[JPT][hapmap]
rs60698775	0.98[ASN][1000 genomes]
rs7018907	0.87[EUR][1000 genomes]
rs7020056	0.80[ASW][hapmap];0.81[TSI][hapmap]
rs7027405	0.88[EUR][1000 genomes]
rs7027771	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7028766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7035107	0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7035722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7038640	0.80[ASW][hapmap];0.87[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7047722	0.81[EUR][1000 genomes]
rs72735324	0.98[ASN][1000 genomes]
rs72735326	0.98[ASN][1000 genomes]
rs7853904	0.88[ASW][hapmap];0.87[CEU][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs7861186	0.89[ASW][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs7862858	0.93[ASN][1000 genomes]
rs9886821	0.80[ASW][hapmap];0.81[TSI][hapmap]
rs9919074	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

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	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10987747	C9orf130	cis	cerebellum	SCAN
rs10987747	ANKS6	Cis_1M	lymphoblastoid	RTeQTL
rs10987747	ZNF189	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101558400-101563800	Weak transcription	Fetal Brain Male	brain
2	chr9:101559400-101564000	Weak transcription	K562	blood
3	chr9:101559600-101564000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:101559600-101564200	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:101559600-101565200	Weak transcription	Esophagus	oesophagus
6	chr9:101559600-101567600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:101559600-101567800	Weak transcription	Stomach Mucosa	stomach
8	chr9:101559600-101569000	Weak transcription	Pancreas	Pancrea
9	chr9:101559600-101569600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:101562000-101563000	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr9:101562200-101563000	Enhancers	Osteobl	bone
12	chr9:101562400-101564200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:101562600-101564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:101562600-101569400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:101562800-101563800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr9:101562800-101564000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:101562800-101564200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:101562800-101564200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr9:101562800-101564200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:101562800-101564400	Weak transcription	H1 Cell Line	embryonic stem cell

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