Variant report

Variant	rs6458086
Chromosome Location	chr6:38901196-38901197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:38901131-38901751	A549	lung:	n/a	n/a
2	RAD21	chr6:38901176-38901666	MCF-7	breast:	n/a	n/a
3	CTCF	chr6:38901140-38901290	A549	lung:	n/a	n/a
4	SMC3	chr6:38901195-38901507	HepG2	liver:	n/a	n/a
5	RAD21	chr6:38901111-38901628	HCT-116	colon:	n/a	n/a
6	CTCF	chr6:38901173-38901575	HepG2	liver:	n/a	n/a
7	RAD21	chr6:38901087-38901719	MCF-7	breast:	n/a	n/a
8	CTCF	chr6:38901078-38901705	HCT-116	colon:	n/a	n/a
9	RAD21	chr6:38901134-38901547	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr6:38901103-38901712	MCF-7	breast:	n/a	n/a
11	RAD21	chr6:38901156-38901588	ECC-1	luminal epithelium:	n/a	n/a
12	RAD21	chr6:38901116-38901711	HCT-116	colon:	n/a	n/a
13	CTCF	chr6:38901086-38901608	MCF-7	breast:	n/a	n/a
14	RAD21	chr6:38901020-38901700	SK-N-SH	brain:	n/a	n/a
15	CTCF	chr6:38900973-38901714	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr6:38901169-38901772	MCF-7	breast:	n/a	chr6:38901725-38901735 chr6:38901274-38901281
17	RAD21	chr6:38901047-38901618	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:38773740..38774704-chr6:38901124..38901864,4	MCF-7	breast:
2	chr6:38896535..38899367-chr6:38900906..38902876,2	MCF-7	breast:
3	chr6:38901008..38902530-chr6:38905671..38907488,2	K562	blood:
4	chr6:38763255..38763863-chr6:38901115..38901700,2	MCF-7	breast:
5	chr6:38839518..38840375-chr6:38900813..38901849,3	MCF-7	breast:
6	chr6:38839463..38840459-chr6:38901033..38901837,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231150	TF binding region
ENSG00000231150	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16891271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823429	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs4452640	0.84[CHB][hapmap];0.87[CHD][hapmap]
rs4711561	0.90[CHB][hapmap]
rs4711565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4714199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57355402	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7757442	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv885821	chr6:38843970-39039503	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv462918	chr6:38875752-38901236	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv602961	chr6:38875752-38901236	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6458086	TSPO2	cis	cerebellum	SCAN
rs6458086	NPM2	trans	parietal	SCAN
rs6458086	SLC26A8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38900800-38901600	Enhancers	Fetal Intestine Large	intestine
2	chr6:38900800-38901600	Enhancers	Fetal Intestine Small	intestine

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