Variant report

Variant	rs10275587
Chromosome Location	chr7:146269716-146269717
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10216262	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10236561	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap]
rs10236933	1.00[CEU][hapmap]
rs10243142	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10249254	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10249436	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10262018	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10262146	1.00[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs10262956	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs10268628	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10272562	0.94[CEU][hapmap]
rs10273967	0.89[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs10280967	0.86[JPT][hapmap]
rs10282256	0.93[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap]
rs10487930	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs10808039	0.84[CHB][hapmap]
rs12532419	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap]
rs168327	0.89[CHB][hapmap]
rs2098126	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2191295	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs2245916	0.89[CHB][hapmap];0.85[ASN][1000 genomes]
rs2693392	0.89[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs2693394	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs2693405	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs347181	0.84[CHB][hapmap]
rs347183	0.90[CHB][hapmap]
rs402278	0.84[CHB][hapmap]
rs4726793	0.89[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs6464768	0.89[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap]
rs6959655	0.87[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap]
rs725717	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7781022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7789059	0.84[CHB][hapmap]
rs802008	0.95[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap]
rs802009	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs802012	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap]
rs802013	0.89[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.81[TSI][hapmap]
rs802019	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs9640229	0.95[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap]
rs971808	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017138	chr7:146102286-146318562	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1028798	chr7:146138480-146318562	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	nsv608931	chr7:146189057-146274427	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1032959	chr7:146193191-146351005	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv934014	chr7:146212698-146400508	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1028701	chr7:146226298-146269716	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv1025948	chr7:146252115-146393151	Weak transcription Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv948895	chr7:146260214-146348562	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10275587	TPK1	cis	cerebellum	SCAN
rs10275587	PDIA4	cis	parietal	SCAN
rs10275587	TPK1	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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