Variant report

Variant	rs1935372
Chromosome Location	chr9:99985788-99985789
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	chr9:99985067..99987314-chr9:99998375..100001266,2	K562	blood:

Variant related genes	Relation type
ENSG00000203279	Chromatin interaction
ENSG00000254483	Chromatin interaction
ENSG00000254876	Chromatin interaction
ENSG00000197816	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10115798	0.85[EUR][1000 genomes]
rs10116404	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217229	0.82[EUR][1000 genomes]
rs10217329	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733584	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739337	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739365	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759542	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759547	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759605	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10759610	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817300	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817306	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817361	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817403	0.86[ASN][1000 genomes]
rs10981362	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10981528	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981537	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10981551	0.86[ASN][1000 genomes]
rs10981557	0.86[ASN][1000 genomes]
rs10981560	0.86[ASN][1000 genomes]
rs12683119	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1462092	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1857084	0.85[ASN][1000 genomes]
rs2255135	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255139	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255244	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2401382	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447287	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447288	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447289	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2447290	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2487874	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2487875	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2502646	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2615144	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795363	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795366	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795369	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2795370	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818236	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818237	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818240	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818241	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818242	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2818244	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2859564	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2888960	0.83[EUR][1000 genomes]
rs3953686	0.83[AFR][1000 genomes]
rs3953688	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994559	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994561	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3994562	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4433262	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4437755	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4524907	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4615708	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4742683	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4743067	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6477982	0.85[ASN][1000 genomes]
rs6477988	0.85[ASN][1000 genomes]
rs6477993	0.85[ASN][1000 genomes]
rs6478008	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6478043	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478044	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478048	0.82[EUR][1000 genomes]
rs6478051	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478054	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478055	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6478059	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7020002	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7020144	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021895	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7023087	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026287	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033212	0.86[EUR][1000 genomes]
rs7033642	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7038353	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7047367	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71491754	0.81[EUR][1000 genomes]
rs725228	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs725229	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs752243	0.86[ASN][1000 genomes]
rs7850473	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7855385	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860264	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7867330	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7868052	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868295	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868312	0.83[EUR][1000 genomes]
rs7875158	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7875296	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9299202	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9408859	0.82[EUR][1000 genomes]
rs9409139	0.83[EUR][1000 genomes];0.86[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	nsv931946	chr9:99895658-100005099	Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv893607	chr9:99906545-99996548	Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893608	chr9:99906545-100005128	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1935372	RP11-23J9.4	cis	Artery Tibial	GTEx
rs1935372	CCDC180	cis	Artery Tibial	GTEx
rs1935372	RP11-520B13.4	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99985200-99992000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:99985200-99995000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:99985400-99985800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:99985400-99985800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
5	chr9:99985400-99985800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr9:99985600-99986000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
7	chr9:99985600-99986000	Enhancers	iPS-20b Cell Line	embryonic stem cell

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