Variant report

Variant	rs6940480
Chromosome Location	chr6:39251648-39251649
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39245598..39248423-chr6:39251437..39253909,2	K562	blood:
2	chr6:39196048..39198749-chr6:39250346..39251924,2	MCF-7	breast:
3	chr6:39246289..39249933-chr6:39249942..39252765,4	MCF-7	breast:
4	chr6:39196660..39199150-chr6:39250070..39252621,3	K562	blood:
5	chr6:39251247..39254688-chr6:39261897..39265141,3	K562	blood:
6	chr6:39196660..39199150-chr6:39250070..39252621,2	K562	blood:
7	chr6:39249494..39252314-chr6:39258691..39261153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10807205	0.82[GIH][hapmap]
rs12194951	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs12197500	0.89[ASN][1000 genomes]
rs12201021	0.86[ASN][1000 genomes]
rs12214300	0.86[ASN][1000 genomes]
rs12214342	0.86[ASN][1000 genomes]
rs16891847	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16891848	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1885619	0.90[JPT][hapmap]
rs2395721	0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap]
rs2758862	0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2758875	0.95[ASN][1000 genomes]
rs2815022	0.85[ASN][1000 genomes]
rs34625110	0.86[ASN][1000 genomes]
rs9349112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9349113	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367000	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9367001	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9367002	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9380846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394581	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs9394582	0.93[ASN][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	nsv830644	chr6:39116530-39325980	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1022974	chr6:39120271-39277553	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv830645	chr6:39227601-39408310	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6940480	FOXP4	cis	cerebellum	SCAN
rs6940480	TMEM217	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39248400-39263400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:39248400-39263400	Weak transcription	Right Atrium	heart
3	chr6:39248800-39252800	Weak transcription	Spleen	Spleen
4	chr6:39249600-39253200	Weak transcription	Gastric	stomach
5	chr6:39249800-39251800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr6:39250000-39251800	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr6:39250600-39252800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:39251000-39258800	Weak transcription	H9 Cell Line	embryonic stem cell

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