Variant report

Variant	rs1603404
Chromosome Location	chr5:154408020-154408021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr5:154407635-154408034	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr5:154407501-154408104	A549	lung:	n/a	n/a
3	RAD21	chr5:154407523-154408027	A549	lung:	n/a	n/a
4	RAD21	chr5:154407406-154408055	HCT-116	colon:	n/a	n/a
5	RAD21	chr5:154407580-154408084	HCT-116	colon:	n/a	n/a
6	RAD21	chr5:154407532-154408065	MCF-7	breast:	n/a	n/a
7	RAD21	chr5:154407515-154408028	HepG2	liver:	n/a	n/a
8	CTCF	chr5:154407454-154408056	MCF-7	breast:	n/a	n/a
9	CTCF	chr5:154407489-154408074	HCT-116	colon:	n/a	n/a
10	SETDB1	chr5:154407893-154408688	U2OS	brain:	n/a	n/a
11	RAD21	chr5:154407411-154408021	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:154350796..154352485-chr5:154407366..154409300,2	MCF-7	breast:
2	chr5:154346758..154347900-chr5:154407299..154408191,5	MCF-7	breast:
3	chr5:154351810..154352823-chr5:154407320..154408737,6	MCF-7	breast:
4	chr5:154351777..154353155-chr5:154407250..154408188,7	MCF-7	breast:
5	chr5:154402654..154405325-chr5:154405571..154408812,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000221131	TF binding region
ENSG00000221131	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10057198	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2431154	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431156	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286601	0.95[CEU][hapmap];0.85[JPT][hapmap]
rs286615	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs286616	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs286619	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs286620	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286626	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs286630	0.82[ASN][1000 genomes]
rs286631	0.82[ASN][1000 genomes]
rs287121	0.82[ASN][1000 genomes]
rs287123	0.82[ASN][1000 genomes]
rs287124	0.82[ASN][1000 genomes]
rs28775325	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580126	0.90[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs664586	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7443026	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv883058	chr5:154375465-154432580	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	esv2762561	chr5:154403211-154408886	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	esv3374550	chr5:154403808-154421409	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	esv3410951	chr5:154403808-154427370	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1603404	HAVCR1	cis	cerebellum	SCAN
rs1603404	MFAP3	cis	parietal	SCAN
rs1603404	MFAP3	cis	cerebellum	SCAN
rs1603404	TIMD4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154404000-154413400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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