Variant report

Variant	rs3799678
Chromosome Location	chr6:49603016-49603017
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:49537454..49540183-chr6:49601842..49604418,2	K562	blood:
2	chr6:49602202..49605447-chr6:49703297..49710547,8	K562	blood:
3	chr6:49583015..49585181-chr6:49601659..49604090,2	K562	blood:
4	chr6:49602139..49603788-chr6:49812242..49813992,2	K562	blood:
5	chr6:49602446..49604105-chr6:49643919..49646864,2	K562	blood:
6	chr6:49602100..49604393-chr6:49661668..49664483,3	K562	blood:
7	chr6:49601488..49603926-chr6:49681926..49683721,2	K562	blood:
8	chr6:49500000..49503895-chr6:49600238..49603257,3	K562	blood:
9	chr6:49602324..49604194-chr6:49642993..49645469,2	MCF-7	breast:
10	chr6:49602379..49604164-chr6:49769811..49771927,2	K562	blood:
11	chr6:49601909..49605014-chr6:49702815..49705548,4	K562	blood:
12	chr6:49602186..49604393-chr6:49661752..49664483,3	K562	blood:
13	chr6:49602829..49604355-chr6:49799539..49801206,2	K562	blood:
14	chr6:49602868..49604498-chr6:49805290..49807651,2	K562	blood:
15	chr6:49601828..49604447-chr6:49633369..49636416,3	K562	blood:
16	chr6:49600996..49604201-chr6:49633369..49637658,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000096006	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs13198157	0.85[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2145331	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2180723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396917	0.85[EUR][1000 genomes]
rs2396918	0.84[CEU][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs2518103	0.90[CHB][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2753076	0.88[ASN][1000 genomes]
rs2753078	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2753080	0.88[ASN][1000 genomes]
rs360562	0.80[CEU][hapmap]
rs3799677	0.88[ASN][1000 genomes]
rs4367380	0.88[ASN][1000 genomes]
rs4495269	0.85[ASN][1000 genomes]
rs62412402	0.88[ASN][1000 genomes]
rs6901845	0.88[ASN][1000 genomes]
rs6904365	0.88[ASN][1000 genomes]
rs6917380	0.82[EUR][1000 genomes]
rs6918589	0.88[ASN][1000 genomes]
rs6918893	0.81[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs6923940	0.88[ASN][1000 genomes]
rs6934730	0.88[ASN][1000 genomes]
rs6934867	0.88[ASN][1000 genomes]
rs7746868	0.84[CEU][hapmap];0.91[GIH][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap];0.84[EUR][1000 genomes]
rs7753483	0.88[ASN][1000 genomes]
rs7753489	0.88[ASN][1000 genomes]
rs9395522	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs9463521	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9463522	0.88[ASN][1000 genomes]
rs9463525	0.88[ASN][1000 genomes]
rs9463526	0.88[ASN][1000 genomes]
rs9463527	0.87[ASN][1000 genomes]
rs9463528	0.88[ASN][1000 genomes]
rs9463529	0.88[ASN][1000 genomes]
rs9463530	0.88[ASN][1000 genomes]
rs9473628	0.88[ASN][1000 genomes]
rs9473631	0.88[ASN][1000 genomes]
rs9473632	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024959	chr6:49290141-49652124	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1021136	chr6:49295037-49631278	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv933942	chr6:49480550-50004231	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv933833	chr6:49515134-49961765	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3799678	C6orf141	cis	cerebellum	SCAN
rs3799678	OPN5	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49596800-49603800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:49601800-49604600	Active TSS	K562	blood
3	chr6:49601800-49607000	Weak transcription	HepG2	liver

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