Variant report

Variant	rs925487
Chromosome Location	chr9:100636398-100636399
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	chr9:100634662..100636711-chr9:100679210..100681058,2	K562	blood:
2	chr9:100636360..100639098-chr9:100684329..100685877,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10046805	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10113884	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115216	0.96[CEU][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10116976	1.00[CHB][hapmap]
rs10117642	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10119760	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10119853	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120412	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10122541	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10123699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124220	1.00[ASN][1000 genomes]
rs10512255	0.96[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10739526	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10759975	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759981	1.00[AFR][1000 genomes];0.99[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	0.81[AMR][1000 genomes]
rs10818133	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10818175	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10818213	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10818241	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10984009	1.00[CHD][hapmap]
rs10984103	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10984230	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10984235	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10984253	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12004762	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12006522	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12341377	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12342417	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12343182	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12347191	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12348304	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12348691	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12550872	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13286291	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13287360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13299924	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1443435	0.92[CEU][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1443436	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1561957	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1561961	0.92[CEU][hapmap];0.92[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1867277	0.81[AMR][1000 genomes]
rs1867278	0.88[CEU][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap]
rs1867280	0.81[AMR][1000 genomes]
rs1955143	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955144	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1955145	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2120264	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2401639	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2417575	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2417576	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28703314	0.84[EUR][1000 genomes]
rs3021526	0.81[AMR][1000 genomes]
rs35324451	0.81[EUR][1000 genomes]
rs3758248	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3758249	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3758251	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3808893	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3824495	0.96[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4255258	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460498	0.86[AMR][1000 genomes];0.83[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];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743142	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6478413	1.00[ASN][1000 genomes]
rs6478437	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6478445	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478469	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6478471	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7022148	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7027221	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7031386	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7032086	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7032114	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7034249	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7034336	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7034648	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7036589	0.96[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7037175	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7037324	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7038998	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7044121	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7044799	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7048255	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7851552	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7860144	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7866436	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7868534	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7871887	1.00[CHD][hapmap]
rs894673	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs907577	0.92[CEU][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs907581	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299258	0.96[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9775370	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs993501	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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
rs925487	C9orf156	cis	cerebellum	SCAN
rs925487	C9orf156	cis	Frontal Cortex	GTEx
rs925487	TSTD2	cis	parietal	SCAN
rs925487	C9orf156	cis	Temporal Cortex	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100631800-100639400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:100634800-100637200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:100635800-100636400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:100635800-100636400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:100635800-100636600	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr9:100635800-100636600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:100635800-100636800	Enhancers	Hela-S3	cervix
8	chr9:100635800-100638400	Enhancers	Esophagus	oesophagus
9	chr9:100635800-100640400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:100636000-100636400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr9:100636000-100638800	Enhancers	NHEK	skin
12	chr9:100636000-100639200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:100636000-100639200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:100636000-100640400	Enhancers	HMEC	breast
15	chr9:100636200-100636400	Enhancers	HSMM	muscle
16	chr9:100636200-100636600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr9:100636200-100636600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
18	chr9:100636200-100636600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:100636200-100636800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:100636200-100638400	Enhancers	A549	lung

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