Variant report

Variant	rs13299166
Chromosome Location	chr9:98595531-98595532
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98594615..98596489-chr9:98611453..98613393,2	K562	blood:
2	chr9:98594398..98596739-chr9:98636652..98638616,2	K562	blood:
3	chr9:98594554..98597338-chr9:98610214..98612721,2	MCF-7	breast:
4	chr9:98594398..98598595-chr9:98636389..98638678,4	K562	blood:
5	chr9:98585752..98588064-chr9:98594275..98596472,2	MCF-7	breast:
6	chr9:98591198..98593705-chr9:98595465..98597908,2	K562	blood:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10115110	0.81[AMR][1000 genomes]
rs10117340	0.86[CEU][hapmap];0.81[CHB][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs10125109	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10512245	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10739622	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10739705	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10760189	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760261	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10760262	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10760269	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10760679	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10818574	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10818746	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10818899	0.90[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10819650	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10819663	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10819668	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10819720	0.81[EUR][1000 genomes]
rs10985156	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985499	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10985769	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10987963	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10988755	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10988817	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1195130	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11998982	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12000073	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12340954	0.80[AMR][1000 genomes]
rs12343734	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12345187	0.86[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12347675	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12348051	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12349742	0.86[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1327996	0.85[CHB][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1327997	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13289466	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13294931	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026031	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2296858	0.81[AMR][1000 genomes]
rs2405134	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2405371	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2405372	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2943532	0.91[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs589362	0.90[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs596413	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs603947	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs617187	0.91[CEU][hapmap];0.91[CHB][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs623438	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs624075	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs625105	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62559026	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62559767	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs640297	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6478977	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs649819	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs657451	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs666093	0.91[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs667705	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs671058	0.90[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs682682	0.91[CHB][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs684455	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs686048	0.86[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs689619	0.86[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs689696	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs689697	0.86[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs689710	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs689738	0.84[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs689744	0.81[AMR][1000 genomes]
rs689761	0.86[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs689804	0.94[CEU][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs689860	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs689911	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs689986	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs690056	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs690063	0.94[CEU][hapmap];0.84[CHB][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs690286	0.81[AMR][1000 genomes]
rs690495	0.91[CEU][hapmap];0.91[CHB][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs690528	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs690633	0.86[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs694230	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs700962	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7847393	0.80[AMR][1000 genomes]
rs7847983	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7852346	0.86[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7871709	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816670	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816672	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816673	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816674	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816675	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816677	0.83[GIH][hapmap]
rs816678	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816680	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816682	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs816683	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816684	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966217	0.87[AMR][1000 genomes];0.89[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs13299166	ERCC6L2	cis	Artery Tibial	GTEx
rs13299166	LOC286353	cis	multi-tissue	Pritchard
rs13299166	C9orf102	cis	multi-tissue	Pritchard
rs13299166	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs13299166	C9orf130	cis	parietal	SCAN
rs13299166	ERCC6L2	cis	Adipose Subcutaneous	GTEx
rs13299166	C9orf130	cis	cerebellum	SCAN
rs13299166	C9orf130	cis	lymphoblastoid	seeQTL
rs13299166	C9orf102	cis	lymphoblastoid	seeQTL
rs13299166	IPPK	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98570800-98601400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:98576000-98596000	Weak transcription	Aorta	Aorta
3	chr9:98591200-98596600	Weak transcription	Fetal Lung	lung
4	chr9:98592400-98597000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:98594000-98611000	Weak transcription	Colonic Mucosa	Colon
6	chr9:98594200-98601800	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:98594400-98610000	Weak transcription	Fetal Stomach	stomach
8	chr9:98594600-98599600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:98594600-98601600	Weak transcription	Right Atrium	heart
10	chr9:98594600-98610000	Weak transcription	Fetal Intestine Small	intestine
11	chr9:98595000-98596200	Weak transcription	Ovary	ovary
12	chr9:98595000-98597200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:98595200-98595600	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:98595200-98595600	Weak transcription	Stomach Smooth Muscle	stomach

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