Variant report

Variant	rs2777860
Chromosome Location	chr9:72028323-72028324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10511966	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
rs10867682	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs10867768	0.85[CEU][hapmap]
rs11138902	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs11139065	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap]
rs11139224	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11139245	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11139246	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11139274	0.85[CEU][hapmap]
rs11139289	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11139293	0.86[CEU][hapmap]
rs11139294	0.85[CEU][hapmap];0.98[TSI][hapmap]
rs1228285	0.80[AMR][1000 genomes]
rs1236984	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12378157	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs12378318	0.85[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap]
rs12551899	0.81[JPT][hapmap]
rs12553491	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
rs13286303	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes]
rs13286400	0.91[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.98[TSI][hapmap]
rs13288354	0.82[CEU][hapmap]
rs13289730	0.84[CEU][hapmap]
rs13290847	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
rs13290881	0.82[JPT][hapmap]
rs13291679	0.84[JPT][hapmap]
rs13291843	0.85[CEU][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
rs13296504	0.91[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs13297121	0.85[JPT][hapmap]
rs1330326	0.85[CEU][hapmap]
rs1330331	0.85[CEU][hapmap]
rs1475641	0.85[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.98[TSI][hapmap]
rs17412941	0.82[JPT][hapmap];0.88[YRI][hapmap]
rs1757961	0.85[ASN][1000 genomes]
rs1761284	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1855529	0.82[JPT][hapmap]
rs2253778	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297420	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2777864	0.82[AMR][1000 genomes]
rs3897757	0.81[ASN][1000 genomes]
rs4307408	0.86[JPT][hapmap]
rs4351475	0.86[JPT][hapmap];0.88[YRI][hapmap]
rs4744884	0.85[JPT][hapmap];0.87[YRI][hapmap]
rs4744885	0.81[JPT][hapmap]
rs4744893	0.91[JPT][hapmap];0.88[YRI][hapmap]
rs4744898	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744899	0.81[ASN][1000 genomes]
rs7025896	0.85[CEU][hapmap]
rs7028920	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs7853058	0.81[JPT][hapmap]
rs867365	0.91[JPT][hapmap];0.88[YRI][hapmap]
rs867366	0.91[JPT][hapmap]
rs9410534	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9410823	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817406	chr9:71675454-72179318	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv893429	chr9:71961923-72047337	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv893430	chr9:71968730-72036369	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1047593	chr9:71971536-72180583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1035633	chr9:71995963-72176984	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893431	chr9:72003036-72048098	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv8522	chr9:72009272-72034735	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv2757340	chr9:72018246-72048098	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2759694	chr9:72018246-72048098	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv893432	chr9:72028323-72056397	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2777860	C9orf71	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72026800-72028400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:72027000-72028400	Enhancers	Esophagus	oesophagus
3	chr9:72027000-72040000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:72027800-72028400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:72027800-72028400	Enhancers	Brain Angular Gyrus	brain
6	chr9:72027800-72028400	Enhancers	Brain Cingulate Gyrus	brain
7	chr9:72028000-72028400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:72028000-72028400	Enhancers	Lung	lung
9	chr9:72028000-72028400	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr9:72028200-72028400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr9:72028200-72028400	Enhancers	Stomach Smooth Muscle	stomach
12	chr9:72028200-72028600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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