Variant report

Variant	rs708109
Chromosome Location	chr1:228190657-228190658
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:228187251..228191319-chr1:228259829..228263819,5	MCF-7	breast:
2	chr1:228189000..228190895-chr1:228269469..228271693,2	MCF-7	breast:
3	chr1:228190330..228192732-chr1:228296220..228298722,2	MCF-7	breast:
4	chr1:228185587..228188986-chr1:228190632..228193211,3	MCF-7	breast:
5	chr1:228190431..228192672-chr1:228192836..228195791,3	K562	blood:
6	chr1:228189312..228191341-chr1:228252791..228255165,2	MCF-7	breast:
7	chr1:228190036..228193608-chr1:228195528..228197492,3	MCF-7	breast:
8	chr1:228190517..228193309-chr1:228296399..228298991,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143761	Chromatin interaction
ENSG00000162910	Chromatin interaction
ENSG00000154342	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10442629	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11584326	0.94[ASN][1000 genomes]
rs1342350	1.00[YRI][hapmap]
rs1636195	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1636196	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1745413	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1774757	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2262292	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2485254	0.84[ASN][1000 genomes]
rs2796055	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2872361	1.00[YRI][hapmap]
rs3094910	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3094911	1.00[CEU][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes]
rs4394650	1.00[YRI][hapmap]
rs587000	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs601050	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs662658	0.84[ASN][1000 genomes]
rs680148	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs681824	0.84[ASN][1000 genomes]
rs697761	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs697762	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs697763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs708108	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs708110	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708113	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs708118	1.00[CEU][hapmap];0.90[TSI][hapmap];0.97[EUR][1000 genomes]
rs708121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs708123	1.00[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs708124	1.00[CEU][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs849900	1.00[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
7	nsv947387	chr1:228140028-228206630	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
10	nsv945349	chr1:228186556-228245135	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs708109	OBSCN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
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