Variant report

Variant	rs2324974
Chromosome Location	chr3:86027715-86027716
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10084664	1.00[CEU][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs11918000	0.96[ASN][1000 genomes]
rs11922573	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11924652	0.83[EUR][1000 genomes]
rs12714643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13070277	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13316083	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13319689	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13320560	1.00[CEU][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap]
rs13320610	1.00[CEU][hapmap]
rs13327074	0.88[TSI][hapmap]
rs2324979	0.83[GIH][hapmap]
rs28708559	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34553213	0.81[EUR][1000 genomes]
rs35143900	0.80[EUR][1000 genomes]
rs35215849	0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35684639	0.82[EUR][1000 genomes]
rs4443171	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4499617	0.81[EUR][1000 genomes]
rs6549060	0.80[EUR][1000 genomes]
rs6762778	0.80[EUR][1000 genomes]
rs6765959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6766354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6771277	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6782241	0.83[EUR][1000 genomes]
rs6805498	0.86[YRI][hapmap]
rs7613116	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7619493	0.86[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7630558	0.85[GIH][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs7646410	1.00[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs9309995	0.83[TSI][hapmap]
rs9309998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9310001	0.81[GIH][hapmap]
rs9810027	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9812103	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9816329	0.85[GIH][hapmap]
rs9819556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9828350	0.88[TSI][hapmap]
rs9829960	0.83[GIH][hapmap];0.94[TSI][hapmap]
rs9831465	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs9837508	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9840565	1.00[CEU][hapmap];0.87[LWK][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs9845052	0.86[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9856754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9861174	0.92[GIH][hapmap]
rs9866277	0.86[GIH][hapmap];0.94[TSI][hapmap]
rs9866543	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9874892	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9876301	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9876425	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880964	0.81[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9881057	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9881372	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	esv3376568	chr3:86024662-86028360	Enhancers Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2324974	S100A3	trans	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86027000-86027800	Enhancers	Brain Cingulate Gyrus	brain
2	chr3:86027000-86027800	Enhancers	Brain Hippocampus Middle	brain
3	chr3:86027200-86028000	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr3:86027600-86028000	Enhancers	Brain Substantia Nigra	brain
5	chr3:86027600-86028600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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