Variant report

Variant	rs1360064
Chromosome Location	chr9:98608989-98608990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98607376..98610344-chr9:98635067..98637790,2	K562	blood:
2	chr9:98602627..98604199-chr9:98606124..98609102,2	K562	blood:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10983321	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10988581	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10988792	0.85[MKK][hapmap];0.95[TSI][hapmap]
rs10988804	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11787559	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11790370	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11790491	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11793298	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11794054	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12001	0.89[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12683310	0.81[EUR][1000 genomes]
rs12683634	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12685221	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12685807	0.89[GIH][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs12686222	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12686457	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16910262	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16910296	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16910298	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16910418	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1831228	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1999023	0.90[CEU][hapmap];0.90[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2026032	0.80[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2069053	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2274654	0.86[GIH][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap]
rs34533243	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3780574	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4532708	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4742775	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742781	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743372	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743391	0.81[EUR][1000 genomes]
rs4743418	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4743436	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4743472	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7048414	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73536517	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73656544	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7868270	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1360064	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs1360064	LINC00476	cis	Esophagus Mucosa	GTEx
rs1360064	LINC00476	cis	Whole Blood	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98594000-98611000	Weak transcription	Colonic Mucosa	Colon
2	chr9:98594400-98610000	Weak transcription	Fetal Stomach	stomach
3	chr9:98594600-98610000	Weak transcription	Fetal Intestine Small	intestine
4	chr9:98596200-98616400	Weak transcription	Fetal Brain Female	brain
5	chr9:98596200-98619200	Weak transcription	Fetal Heart	heart
6	chr9:98596400-98619400	Weak transcription	Right Ventricle	heart
7	chr9:98599200-98614400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:98602000-98632800	Weak transcription	Left Ventricle	heart
9	chr9:98602000-98636000	Weak transcription	Lung	lung
10	chr9:98602400-98619400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:98602600-98618800	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:98602600-98619400	Weak transcription	Psoas Muscle	Psoas
13	chr9:98602600-98620200	Weak transcription	Small Intestine	intestine
14	chr9:98602800-98614400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:98602800-98619000	Weak transcription	Ovary	ovary
16	chr9:98603000-98610200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:98603200-98611200	Weak transcription	Liver	Liver
18	chr9:98604400-98621200	Weak transcription	Primary T cells from cord blood	blood
19	chr9:98607000-98610000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:98607400-98612000	Weak transcription	Fetal Intestine Large	intestine
21	chr9:98607400-98621600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr9:98607800-98609000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:98607800-98609000	Enhancers	Fetal Lung	lung
24	chr9:98608000-98614200	Weak transcription	NHLF	lung
25	chr9:98608200-98609000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr9:98608200-98609000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:98608200-98614400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:98608400-98610200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:98608400-98614200	Weak transcription	Brain Substantia Nigra	brain
30	chr9:98608600-98614200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:98608800-98609000	Enhancers	Spleen	Spleen

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