Variant report

Variant	rs7599837
Chromosome Location	chr2:77305123-77305124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10174161	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10181919	0.90[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap]
rs10198799	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs11126580	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11126582	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11126586	0.91[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs11126589	0.95[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs11903423	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap]
rs13412552	0.87[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap]
rs13421983	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13422002	0.95[CEU][hapmap];0.86[CHB][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13431979	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1374391	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1374395	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1823131	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1921733	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2860082	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2860940	0.95[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2860941	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28739330	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4455181	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56050325	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56120121	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56125553	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56357290	0.81[AMR][1000 genomes]
rs6547121	0.86[CEU][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap]
rs6725731	0.85[CHB][hapmap];0.87[YRI][hapmap]
rs6730095	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap]
rs6746253	0.95[CEU][hapmap];0.81[AMR][1000 genomes]
rs6750737	0.91[CEU][hapmap];0.97[GIH][hapmap];0.80[TSI][hapmap]
rs6750865	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs715280	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7570003	0.95[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs7583894	0.95[CEU][hapmap];0.83[CHB][hapmap]
rs7586053	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs957839	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949670	chr2:77125218-77712607	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1014895	chr2:77263452-77414507	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv874331	chr2:77264354-77305123	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
4	nsv458285	chr2:77276201-77345491	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases
5	nsv582252	chr2:77276201-77345491	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
6	nsv874332	chr2:77288585-77387208	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
7	nsv526121	chr2:77297536-77305123	Enhancers ZNF genes & repeats Weak transcription	n/a	n/a	inside rSNPs	diseases
8	nsv961692	chr2:77302479-77306376	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7599837	USF1	trans	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:77300000-77311600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:77302400-77307400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:77304600-77307800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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