Variant report

Variant	rs993501
Chromosome Location	chr9:100623377-100623378
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	chr9:100622883..100625643-chr9:100642333..100644291,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10046805	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10113884	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115216	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[LWK][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10116976	1.00[CHB][hapmap]
rs10117642	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119760	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10119853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120412	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10122541	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10123699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124220	1.00[ASN][1000 genomes]
rs10512255	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10512256	0.90[LWK][hapmap]
rs1059003	0.90[LWK][hapmap]
rs10739526	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10759975	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759981	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760011	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10760017	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10818124	0.80[EUR][1000 genomes]
rs10818133	0.83[EUR][1000 genomes]
rs10818175	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10818213	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10818241	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10984009	1.00[CHD][hapmap]
rs10984103	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10984230	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10984235	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10984253	0.94[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10984516	0.90[LWK][hapmap]
rs10984532	0.90[LWK][hapmap]
rs10984545	0.90[LWK][hapmap]
rs12004762	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12006522	0.96[CEU][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12341377	0.83[EUR][1000 genomes]
rs12342417	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12343182	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12347191	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12348304	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12348691	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12550872	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13286291	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13287360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13299924	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1348386	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1443432	1.00[ASN][1000 genomes]
rs1443433	1.00[CHD][hapmap]
rs1443434	0.92[CEU][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1443435	0.92[CEU][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1443436	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1561957	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1561961	0.92[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1867278	0.81[CEU][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap]
rs1955143	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955144	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1955145	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2120264	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2401639	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2417575	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2417576	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28703314	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3021526	0.80[EUR][1000 genomes]
rs3758248	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3758249	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3758251	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3808893	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3824495	0.96[CEU][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4255258	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460498	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4743138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4743139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743142	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6478413	1.00[ASN][1000 genomes]
rs6478437	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6478445	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478469	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6478471	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7022148	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7027221	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7031386	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7032086	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7032114	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7034249	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7034336	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7034648	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7036589	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[GIH][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7037175	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7037324	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7038998	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7044121	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044799	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7048255	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7851552	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7851660	0.81[EUR][1000 genomes]
rs7860144	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7866436	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7868534	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7871887	1.00[CHD][hapmap]
rs894673	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs907577	0.92[CEU][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs907581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299258	0.96[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9775370	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs993501	C9orf156	cis	Temporal Cortex	GTEx
rs993501	C9orf156	cis	Frontal Cortex	GTEx
rs993501	TSTD2	cis	parietal	SCAN
rs993501	C9orf156	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100620800-100625800	Weak transcription	Gastric	stomach
2	chr9:100622600-100623600	Enhancers	NHEK	skin
3	chr9:100622800-100623400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:100622800-100623400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:100622800-100623400	Enhancers	HSMM	muscle
6	chr9:100622800-100623600	Enhancers	HSMMtube	muscle
7	chr9:100623000-100623400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:100623200-100623400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr9:100623200-100623400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:100623200-100623400	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr9:100623200-100623400	Bivalent Enhancer	Left Ventricle	heart

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