Variant report

Variant	rs3860304
Chromosome Location	chr1:190235047-190235048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10494633	0.82[CHB][hapmap]
rs10920712	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs10920713	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs1093040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1093088	0.80[AFR][1000 genomes]
rs11577349	0.93[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs11584718	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1171386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs12083426	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12084962	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap]
rs12095554	0.91[EUR][1000 genomes]
rs1442570	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1442571	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1855238	0.83[AFR][1000 genomes]
rs1930767	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs1935877	0.82[AFR][1000 genomes]
rs510498	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs639574	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6662228	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs6668152	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6676702	0.90[EUR][1000 genomes]
rs6679910	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6682679	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6691829	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6695866	0.91[EUR][1000 genomes]
rs6695984	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs72731142	0.91[EUR][1000 genomes]
rs72731143	0.90[EUR][1000 genomes]
rs7545105	0.89[EUR][1000 genomes]
rs815330	0.87[LWK][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548532	chr1:189758772-190371671	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv917005	chr1:189855484-190259380	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv932040	chr1:190005334-190914580	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1003035	chr1:190123195-190291554	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv872756	chr1:190164775-190287713	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1013402	chr1:190197674-190332464	Enhancers ZNF genes & repeats Active TSS Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
7	nsv535246	chr1:190197674-190332464	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3860304	FAM5C	cis	cerebellum	SCAN
rs3860304	PDC	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190228000-190244200	Weak transcription	Fetal Intestine Small	intestine

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