Variant report

Variant	rs863365
Chromosome Location	chr1:158551329-158551330
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1002599	0.85[CHB][hapmap]
rs1032352	0.80[ASN][1000 genomes]
rs10489833	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs10489834	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs10489835	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs10797017	0.92[CEU][hapmap]
rs10797020	0.95[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs10797022	0.80[ASN][1000 genomes]
rs10797023	0.80[ASN][1000 genomes]
rs10797024	0.80[ASN][1000 genomes]
rs10908652	0.85[EUR][1000 genomes]
rs10908656	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10908659	0.86[EUR][1000 genomes]
rs10908663	0.80[ASN][1000 genomes]
rs10908664	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10908680	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs11264989	0.86[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap]
rs11264994	0.83[EUR][1000 genomes]
rs11264998	0.93[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs11265002	0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs11265003	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1157523	0.85[EUR][1000 genomes]
rs1157525	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12041218	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs12080815	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12081915	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12118446	0.80[ASN][1000 genomes]
rs12122663	0.82[ASN][1000 genomes]
rs12133791	0.82[ASN][1000 genomes]
rs12133794	0.82[ASN][1000 genomes]
rs12145401	0.80[ASN][1000 genomes]
rs1342947	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1342958	0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs1418843	0.85[EUR][1000 genomes]
rs1418845	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs1418846	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs1418847	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs1491196	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1573519	0.85[CHB][hapmap]
rs1578761	0.80[ASN][1000 genomes]
rs1578762	0.80[ASN][1000 genomes]
rs1578763	0.80[ASN][1000 genomes]
rs17630699	0.87[EUR][1000 genomes]
rs1873509	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs1873510	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs1873511	0.95[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs1894040	1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs2157687	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2157689	0.87[EUR][1000 genomes]
rs2213947	0.84[EUR][1000 genomes]
rs2317969	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2317970	0.82[ASN][1000 genomes]
rs2873593	0.82[ASN][1000 genomes]
rs2873594	0.82[ASN][1000 genomes]
rs2873595	0.82[ASN][1000 genomes]
rs4276920	0.82[ASN][1000 genomes]
rs4575081	0.82[ASN][1000 genomes]
rs4609418	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4657080	0.85[CHB][hapmap]
rs6657638	0.80[ASN][1000 genomes]
rs6663277	0.80[ASN][1000 genomes]
rs6666609	0.80[ASN][1000 genomes]
rs6670343	0.80[ASN][1000 genomes]
rs6672789	0.80[ASN][1000 genomes]
rs6674656	0.80[ASN][1000 genomes]
rs6697656	0.95[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[ASN][1000 genomes]
rs6699473	0.80[ASN][1000 genomes]
rs7512592	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs7514968	0.80[ASN][1000 genomes]
rs7515245	0.80[ASN][1000 genomes]
rs7518708	0.82[ASN][1000 genomes]
rs7518808	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7525362	0.80[ASN][1000 genomes]
rs7526514	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7533071	0.82[ASN][1000 genomes]
rs7540999	0.82[ASN][1000 genomes]
rs7548349	0.80[ASN][1000 genomes]
rs7549581	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs863345	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs863346	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs863347	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs863351	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs863352	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs863353	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs863356	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs923663	0.82[ASN][1000 genomes]
rs923664	0.82[ASN][1000 genomes]
rs950260	0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs950487	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9651046	0.85[CHB][hapmap]
rs9804005	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv547986	chr1:158520205-158556839	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3491788	chr1:158537183-158725907	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3491789	chr1:158537242-158725858	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs863365	FCRL2	cis	parietal	SCAN
rs863365	DCST2	cis	cerebellum	SCAN
rs863365	IGSF8	cis	cerebellum	SCAN
rs863365	CD5L	cis	parietal	SCAN

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

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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