Variant report

Variant	rs10983321
Chromosome Location	chr9:98549899-98549900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98548275..98549970-chr9:98636593..98639277,2	MCF-7	breast:
2	chr9:98516863..98518461-chr9:98547406..98550399,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10988581	0.87[EUR][1000 genomes]
rs10988804	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs11787559	0.89[EUR][1000 genomes]
rs11790370	0.86[EUR][1000 genomes]
rs11790491	0.85[EUR][1000 genomes]
rs11793298	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11794054	0.87[EUR][1000 genomes]
rs12683634	0.84[EUR][1000 genomes]
rs12685221	0.89[EUR][1000 genomes]
rs1360064	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16910262	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16910296	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16910298	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16910418	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1831228	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1999023	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2026032	0.87[EUR][1000 genomes]
rs2069053	0.85[CEU][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34533243	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3780574	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs4532708	0.84[EUR][1000 genomes]
rs4742775	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4742781	0.85[CEU][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4743372	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4743418	0.87[EUR][1000 genomes]
rs4743436	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs7048414	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73536517	0.87[EUR][1000 genomes]
rs73656544	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7868270	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.83[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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10983321	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs10983321	LINC00476	cis	Whole Blood	GTEx
rs10983321	LINC00476	cis	Esophagus Mucosa	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98535400-98550800	Weak transcription	Right Atrium	heart
2	chr9:98544800-98550400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:98547000-98550200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:98548200-98553600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:98548200-98558400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:98548400-98550800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:98548400-98578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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