Variant report

Variant	rs42481
Chromosome Location	chr8:90837714-90837715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr8:90837700-90837850	GM12878	blood:	n/a	n/a
2	CTCF	chr8:90837700-90837850	HPAF	blood vessel:	n/a	n/a
3	MAFK	chr8:90837467-90837837	HepG2	liver:	n/a	n/a
4	CTCF	chr8:90837660-90837810	HPAF	blood vessel:	n/a	n/a
5	CTCF	chr8:90837700-90837850	HCPEpiC	choroid plexus:	n/a	n/a
6	MAFK	chr8:90837619-90837824	IMR90	lung:	n/a	n/a
7	CTCF	chr8:90837660-90837810	BE2_C	brain:	n/a	n/a
8	RFX5	chr8:90837585-90838692	IMR90	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:90824515..90827081-chr8:90836313..90840458,3	MCF-7	breast:
2	chr8:90835454..90837187-chr8:90837338..90840296,2	MCF-7	breast:
3	chr8:90835014..90836804-chr8:90836875..90838600,2	K562	blood:
4	chr8:90836699..90839189-chr8:90853198..90855476,2	MCF-7	breast:

No data

Variant related genes	Relation type
COX6B1P6	TF binding region
ENSG00000253349	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1003843	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs10112852	0.81[CEU][hapmap]
rs218902	0.81[CEU][hapmap]
rs218907	0.81[CEU][hapmap]
rs218908	0.81[CEU][hapmap]
rs218913	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs218929	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs366867	0.85[ASN][1000 genomes]
rs367640	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs370282	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs374957	0.92[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs376962	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs377897	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs379015	0.90[ASN][1000 genomes]
rs380425	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs381456	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs383592	0.83[GIH][hapmap]
rs386587	0.90[ASN][1000 genomes]
rs388866	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs390536	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs39499	0.81[CEU][hapmap]
rs39500	0.81[CEU][hapmap]
rs39503	0.89[GIH][hapmap]
rs39506	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs39519	0.92[CEU][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs39761	0.81[CEU][hapmap]
rs39771	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs39772	0.93[EUR][1000 genomes]
rs40250	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs402886	0.81[CEU][hapmap]
rs40382	0.85[ASN][1000 genomes]
rs40452	0.81[CEU][hapmap]
rs40453	0.84[GIH][hapmap]
rs40459	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40547	0.86[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs40636	0.80[ASN][1000 genomes]
rs40638	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs410663	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs411279	0.84[GIH][hapmap]
rs416324	0.84[GIH][hapmap]
rs418634	0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs419890	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42186	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42346	0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs42490	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs425140	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs425312	0.92[EUR][1000 genomes]
rs426240	0.93[EUR][1000 genomes]
rs427854	0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs43134	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs43135	0.85[ASN][1000 genomes]
rs43136	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs43225	0.81[CEU][hapmap]
rs43229	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs432457	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs438485	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs447618	0.81[CEU][hapmap];0.89[GIH][hapmap]
rs447989	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
2	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv891182	chr8:90785685-90888786	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv520356	chr8:90823687-90857989	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv968495	chr8:90835687-90842298	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv2761448	chr8:90837630-90853986	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs42481	OSGIN2	cis	parietal	SCAN
rs42481	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs42481	RIPK2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90828000-90845800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr8:90836400-90837800	Enhancers	Fetal Intestine Large	intestine
3	chr8:90836800-90838200	Enhancers	A549	lung
4	chr8:90836800-90838400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr8:90836800-90839000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr8:90837000-90837800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr8:90837000-90838200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr8:90837000-90838200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:90837000-90838200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr8:90837000-90839000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:90837000-90847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr8:90837200-90838200	Weak transcription	Pancreas	Pancrea
13	chr8:90837200-90838400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr8:90837200-90844600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr8:90837400-90837800	Enhancers	HepG2	liver
16	chr8:90837400-90838200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr8:90837400-90838400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr8:90837600-90838000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr8:90837600-90838000	Weak transcription	Stomach Mucosa	stomach
20	chr8:90837600-90839200	Enhancers	Muscle Satellite Cultured Cells	--

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