Variant report

Variant	rs9395548
Chromosome Location	chr6:49934735-49934736
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr6:49934575-49934897	A549	lung:	n/a	chr6:49934730-49934741
2	CEBPB	chr6:49934561-49934924	Hela-S3	cervix:	n/a	chr6:49934730-49934741
3	CEBPB	chr6:49934640-49934807	HepG2	liver:	n/a	chr6:49934730-49934741
4	CEBPB	chr6:49934572-49934876	K562	blood:	n/a	chr6:49934730-49934741
5	CEBPB	chr6:49934545-49934928	K562	blood:	n/a	chr6:49934730-49934741

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:49930677..49932249-chr6:49932732..49935281,2	K562	blood:

Variant related genes	Relation type
DEFB114	TF binding region
ENSG00000177684	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12197158	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12200124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203532	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1324527	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs1337820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337821	0.94[ASN][1000 genomes]
rs1337822	0.95[ASN][1000 genomes]
rs1337823	0.87[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap]
rs1415732	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1535933	0.83[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1538193	0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1953699	0.88[ASN][1000 genomes]
rs1970303	0.93[ASN][1000 genomes]
rs2039692	0.91[ASN][1000 genomes]
rs2147409	0.92[ASN][1000 genomes]
rs2147410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2181910	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34235414	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3900863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4142072	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs4236101	0.88[ASN][1000 genomes]
rs4711937	0.95[ASN][1000 genomes]
rs4711938	0.95[ASN][1000 genomes]
rs4715151	0.88[ASN][1000 genomes]
rs4715152	0.88[ASN][1000 genomes]
rs4715153	0.88[ASN][1000 genomes]
rs4715164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715165	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs6458719	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.93[ASN][1000 genomes]
rs6927196	0.91[ASN][1000 genomes]
rs7743942	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7747376	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7754156	0.95[ASN][1000 genomes]
rs7760672	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs7766636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776086	0.88[ASN][1000 genomes]
rs7776352	0.88[ASN][1000 genomes]
rs9349509	0.87[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[ASN][1000 genomes]
rs9357636	0.88[ASN][1000 genomes]
rs9357638	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357639	0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs9357641	0.94[ASN][1000 genomes]
rs9367379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369924	0.86[ASN][1000 genomes]
rs9369926	0.93[ASN][1000 genomes]
rs9369928	0.95[ASN][1000 genomes]
rs9381833	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9395543	0.92[ASN][1000 genomes]
rs9395544	0.90[ASN][1000 genomes]
rs9395547	0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[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	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
2	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
3	nsv462944	chr6:49869448-49948059	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv603091	chr6:49869448-49948059	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv970330	chr6:49921724-49940183	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9395548	MUT	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:49931000-49934800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:49933600-49935200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr6:49933600-49935400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr6:49934000-49935000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:49934000-49935000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:49934400-49936800	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr6:49934400-49937600	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr6:49934600-49935200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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