Variant report

Variant	rs7646410
Chromosome Location	chr3:85969391-85969392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10084664	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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514735	0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap]
rs11915638	0.93[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap]
rs11923173	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs11925878	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs11926925	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs12714643	1.00[CEU][hapmap]
rs13070277	1.00[CEU][hapmap]
rs13316083	1.00[CEU][hapmap]
rs13320560	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs13320610	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1448611	0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap]
rs2324974	1.00[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs34553213	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35143900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35215849	0.84[TSI][hapmap]
rs4134358	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4443171	0.89[TSI][hapmap]
rs4499617	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57877306	1.00[ASN][1000 genomes]
rs6549060	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6762778	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6765959	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6766354	1.00[CEU][hapmap]
rs6807918	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72615729	0.90[ASN][1000 genomes]
rs7619493	0.84[TSI][hapmap]
rs7621179	0.94[CHB][hapmap];0.88[CHD][hapmap];0.83[JPT][hapmap]
rs7622544	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs7630558	0.84[TSI][hapmap]
rs9309995	0.84[TSI][hapmap]
rs9309998	1.00[CEU][hapmap]
rs9812103	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs9819556	1.00[CEU][hapmap]
rs9829960	0.84[TSI][hapmap]
rs9831465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840565	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9845052	0.84[TSI][hapmap]
rs9856754	1.00[CEU][hapmap]
rs9861174	0.82[TSI][hapmap]
rs9866277	0.84[TSI][hapmap]
rs9866543	0.90[EUR][1000 genomes]
rs9876301	0.86[EUR][1000 genomes]
rs9876425	0.92[EUR][1000 genomes]
rs9881372	0.91[EUR][1000 genomes]

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	nsv532629	chr3:85763873-86608579	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv877106	chr3:85814620-86006210	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv877107	chr3:85814620-86037162	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv877108	chr3:85870363-86037162	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
5	nsv877109	chr3:85892098-86006210	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv877110	chr3:85892098-86037162	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
7	nsv877111	chr3:85892098-86044224	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	nsv460754	chr3:85917289-86006210	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
9	nsv460755	chr3:85917289-86006210	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
10	nsv590912	chr3:85917289-86006210	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv470727	chr3:85917289-86044224	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
12	nsv590913	chr3:85917289-86044224	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
13	nsv877112	chr3:85964737-86083716	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7646410	S100A3	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85965200-85987000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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