Variant report

Variant	rs9502134
Chromosome Location	chr6:4211534-4211535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89704550..89706161-chr6:4211155..4212675,2	MCF-7	breast:
2	chr6:3741855..3743317-chr6:4210584..4211546,5	K562	blood:
3	chr5:89705777..89706344-chr6:4211154..4211675,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000153140	Chromatin interaction
ENSG00000255647	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1123555	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752585	0.97[EUR][1000 genomes]
rs11753020	1.00[ASN][1000 genomes]
rs11970115	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13197025	0.97[EUR][1000 genomes]
rs13207648	1.00[ASN][1000 genomes]
rs13213431	1.00[ASN][1000 genomes]
rs1327990	1.00[CHD][hapmap]
rs1360811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17137823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1932186	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002920	0.96[EUR][1000 genomes]
rs2002922	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2326472	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34635954	0.98[EUR][1000 genomes]
rs34697725	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34871965	1.00[ASN][1000 genomes]
rs35389479	1.00[ASN][1000 genomes]
rs35801932	0.97[EUR][1000 genomes]
rs35928057	0.96[EUR][1000 genomes]
rs36042165	1.00[ASN][1000 genomes]
rs36099042	1.00[ASN][1000 genomes]
rs6597033	0.97[EUR][1000 genomes]
rs6597034	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6597038	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6912138	0.98[EUR][1000 genomes]
rs6912707	0.97[EUR][1000 genomes]
rs6932643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6933147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938649	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71555837	1.00[ASN][1000 genomes]
rs7743925	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7745239	1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7748217	1.00[YRI][hapmap]
rs7749039	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs7749050	1.00[CEU][hapmap]
rs7749536	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7751774	1.00[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs7761775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770426	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9502132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9502136	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503947	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9503950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9503952	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503955	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503958	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503959	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503979	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503980	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9503981	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9502134	TSPYL5	trans	cerebellum	SCAN
rs9502134	FOXF2	cis	cerebellum	SCAN
rs9502134	CDYL	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4208800-4212400	Weak transcription	Psoas Muscle	Psoas
2	chr6:4208800-4212400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr6:4208800-4212600	Weak transcription	Fetal Heart	heart
4	chr6:4210800-4211600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr6:4210800-4213600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:4211000-4213000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:4211000-4225400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:4211400-4216600	Enhancers	Adipose Nuclei	Adipose

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