Variant report

Variant	rs2054743
Chromosome Location	chr8:50906620-50906621
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10112215	0.87[JPT][hapmap];0.82[AFR][1000 genomes]
rs10112818	0.84[MEX][hapmap];0.89[TSI][hapmap]
rs1023979	0.94[JPT][hapmap]
rs10435582	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10957710	1.00[CEU][hapmap];0.81[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10957737	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10957739	0.86[CHD][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10957741	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs10957742	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11777957	0.87[JPT][hapmap]
rs11783503	0.87[JPT][hapmap]
rs11783631	0.87[JPT][hapmap]
rs12541363	0.87[JPT][hapmap]
rs12541599	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12681482	0.80[AFR][1000 genomes]
rs13255224	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13266009	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13273334	0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1344326	0.87[JPT][hapmap]
rs1352114	0.94[JPT][hapmap];0.80[AFR][1000 genomes]
rs1484805	0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1484806	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1486256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1552316	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1552380	0.82[CHB][hapmap]
rs1601298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1973259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2015043	0.87[JPT][hapmap]
rs2035528	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs203930	0.81[JPT][hapmap]
rs203942	0.81[JPT][hapmap]
rs2086888	0.86[CHD][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2129161	0.87[JPT][hapmap]
rs2129169	0.87[JPT][hapmap]
rs2220157	0.87[JPT][hapmap]
rs2385699	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2385700	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2449963	0.86[CHD][hapmap];0.94[JPT][hapmap]
rs318867	0.94[JPT][hapmap]
rs318913	0.86[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs34179442	0.87[EUR][1000 genomes]
rs4144735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4242456	0.87[JPT][hapmap]
rs4873123	0.87[JPT][hapmap]
rs7010915	0.87[JPT][hapmap]
rs7014520	0.87[JPT][hapmap]
rs7833377	0.94[JPT][hapmap]
rs923058	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs931293	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs931294	0.87[JPT][hapmap]
rs9643689	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9643692	0.83[CHD][hapmap];0.94[JPT][hapmap];0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs971926	0.87[JPT][hapmap]
rs993553	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353749	chr8:50530807-51139242	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv916392	chr8:50827638-51395140	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1022115	chr8:50864995-50981944	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv611311	chr8:50865230-50980320	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv34788	chr8:50873247-50965438	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3479183	chr8:50873277-50965062	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1033098	chr8:50873293-50965692	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv2757272	chr8:50873293-50968942	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv2759613	chr8:50873293-51137995	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3479184	chr8:50873317-50965027	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3479185	chr8:50873317-50965027	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3692982	chr8:50875494-50959622	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1023258	chr8:50877934-50964286	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv818624	chr8:50882830-50945075	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv2758621	chr8:50886593-51137995	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	esv1795686	chr8:50906474-50921942	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2054743	SNTG1	cis	cerebellum	SCAN
rs2054743	EFCAB1	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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