Variant report

Variant	rs3849278
Chromosome Location	chr1:190285536-190285537
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10047048	0.95[AMR][1000 genomes]
rs10494632	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10800937	0.95[AMR][1000 genomes]
rs10920611	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs10920655	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10920677	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10920680	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10920692	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs1148609	0.83[JPT][hapmap]
rs1171045	0.97[GIH][hapmap]
rs1182981	0.81[JPT][hapmap]
rs12072689	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12072690	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12073139	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes]
rs12073296	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12076854	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs12081131	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12090879	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs12093349	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs12406050	0.95[AMR][1000 genomes]
rs12407537	0.95[AMR][1000 genomes]
rs1333319	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1333320	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1333322	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1342909	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs1539473	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1540513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs1557188	1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap]
rs1592245	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap]
rs16832159	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap]
rs16832195	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap]
rs16832220	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap]
rs1831784	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2095171	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs2104927	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap]
rs2293451	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap]
rs2418886	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap]
rs2419063	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3762299	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4373764	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4399162	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes]
rs4845230	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs4845235	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs60812740	0.95[AMR][1000 genomes]
rs61818779	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6665930	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes]
rs6671234	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs6674508	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7416623	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs7535549	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];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs7546329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs7548837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs879963	1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	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
5	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
6	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
7	nsv1004868	chr1:190259314-190303769	Enhancers Active TSS Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	nsv535247	chr1:190259314-190303769	Enhancers Active TSS Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
9	nsv1007121	chr1:190263588-190305514	Active TSS Weak transcription Enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190284600-190288000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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