Variant report

Variant	rs2642505
Chromosome Location	chr7:146361219-146361220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10249351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1072972	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs1072973	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10952649	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs10952650	0.85[CEU][hapmap];0.84[JPT][hapmap]
rs10952651	0.83[CEU][hapmap]
rs10952652	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11773794	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs12530645	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs1389783	0.94[CEU][hapmap];0.85[TSI][hapmap]
rs1494452	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1494458	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1587048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1587049	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs168257	1.00[CEU][hapmap]
rs2109278	0.87[YRI][hapmap]
rs2109280	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2131932	0.89[CEU][hapmap];0.93[CHB][hapmap]
rs2159461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap]
rs2249085	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2372762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2372763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2533082	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2533084	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2533088	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2533108	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2533109	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs2533122	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2642481	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2642483	0.93[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2642484	0.93[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2642485	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2642486	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2642487	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2642488	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs2642490	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs2642495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2642496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2642500	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs2642504	0.93[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs2642515	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2642516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs2642520	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2907673	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs344457	0.89[CEU][hapmap]
rs6944307	0.89[ASN][1000 genomes]
rs6945453	0.93[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs6954014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6959595	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs717171	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs740808	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7802801	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs9640232	0.86[ASN][1000 genomes]
rs9640482	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889391	chr7:146168418-146389259	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1021967	chr7:146199590-146413808	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1015996	chr7:146202073-146419347	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv934014	chr7:146212698-146400508	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1022547	chr7:146226298-146624409	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv996300	chr7:146236230-146663300	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv1025948	chr7:146252115-146393151	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1018605	chr7:146287876-146448400	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv889392	chr7:146292088-146446767	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1027561	chr7:146308783-146762872	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv1034346	chr7:146326815-146367793	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv608939	chr7:146332953-146464965	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv526330	chr7:146342322-146371181	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1021923	chr7:146344105-146442062	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1021542	chr7:146344105-146564397	Enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv817275	chr7:146346102-146475758	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv2761379	chr7:146347722-146448412	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv531439	chr7:146349600-146467532	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv889393	chr7:146353619-146428215	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv970777	chr7:146358313-146369940	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2642505	TPK1	cis	parietal	SCAN

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

No data

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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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