Variant report

Variant	rs2401639
Chromosome Location	chr9:100607837-100607838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100565524..100567505-chr9:100607472..100609592,3	MCF-7	breast:
2	chr9:100602789..100604485-chr9:100606547..100608387,2	K562	blood:
3	chr9:100456538..100459527-chr9:100606763..100609012,2	K562	blood:
4	chr9:100597021..100598744-chr9:100606571..100608440,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10046805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113884	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10117642	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10119760	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10119795	0.81[CHB][hapmap];0.83[YRI][hapmap]
rs10119853	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10120412	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10122541	0.86[AMR][1000 genomes]
rs10123699	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10759975	0.81[EUR][1000 genomes]
rs10759981	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10818124	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10818133	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10818175	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10983853	0.86[CHB][hapmap]
rs10983855	0.86[CHB][hapmap]
rs10983920	0.81[AFR][1000 genomes]
rs10983958	0.90[ASN][1000 genomes]
rs10983959	0.90[ASN][1000 genomes]
rs10984103	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1156850	0.83[ASN][1000 genomes]
rs12238579	0.81[CHB][hapmap]
rs12341377	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342417	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12343182	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12347191	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287360	0.81[EUR][1000 genomes]
rs13299924	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13302470	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1443434	1.00[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443435	1.00[CHB][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443436	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1561958	0.81[CHB][hapmap]
rs1867277	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867278	1.00[CHB][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1867280	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1955143	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955144	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955145	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2120264	0.80[AMR][1000 genomes]
rs2417575	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2417576	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3021526	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3758248	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758249	1.00[CHB][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758251	1.00[CHB][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4297160	0.87[ASN][1000 genomes]
rs4460498	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743139	0.81[EUR][1000 genomes]
rs6478437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478445	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6586	0.81[CHB][hapmap]
rs7033315	0.80[AFR][1000 genomes]
rs7033765	0.87[ASN][1000 genomes]
rs7037175	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7043516	0.82[YRI][hapmap]
rs7045138	0.87[ASN][1000 genomes]
rs7357707	0.80[AFR][1000 genomes]
rs7851552	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851660	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7860144	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7868534	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7870540	0.83[ASN][1000 genomes]
rs7870795	0.93[CHB][hapmap];0.83[ASN][1000 genomes]
rs874004	0.81[AFR][1000 genomes]
rs894673	1.00[CHB][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907577	1.00[CHB][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907581	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs925487	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs993501	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2401639	Hs.43687	cis	multi-tissue	Pritchard

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100607400-100608000	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:100607800-100608000	Bivalent Enhancer	NH-A	brain

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