Variant report

Variant	rs9858931
Chromosome Location	chr3:112616780-112616781
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10511313	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10804504	0.92[CEU][hapmap]
rs10804505	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10804506	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10934191	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10934197	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1114404	0.85[CEU][hapmap]
rs11714354	0.81[EUR][1000 genomes]
rs11717778	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11718878	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720045	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12487198	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487296	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12489734	0.92[CEU][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12490586	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490671	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12633234	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13063847	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13076130	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13092251	0.94[EUR][1000 genomes]
rs13094280	0.92[CEU][hapmap]
rs13323006	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1354055	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860225	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997281	0.92[CEU][hapmap]
rs2220397	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2399437	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399442	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28782232	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34147006	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763318	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6765575	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6786513	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6787688	0.85[CEU][hapmap]
rs6795428	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798395	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6799171	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6805341	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806976	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6807722	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7609699	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7621490	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7639603	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7641119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651207	0.92[CEU][hapmap]
rs9288959	0.92[CEU][hapmap]
rs9288964	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9813901	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9814008	0.92[CEU][hapmap]
rs9815002	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9819621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823692	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9825873	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9826834	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9829184	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9834599	0.92[CEU][hapmap]
rs9838295	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9839592	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9842637	0.82[AMR][1000 genomes]
rs9845041	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846377	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9852286	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852577	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9853006	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9860428	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9863580	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865066	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9868922	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869058	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9871326	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9871605	0.85[CEU][hapmap]
rs9877803	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3501334	chr3:112546820-112648766	Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3501335	chr3:112546820-112648766	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9858931	C3orf17	cis	cerebellum	SCAN
rs9858931	CD200R1	cis	multi-tissue	Pritchard

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112612000-112617400	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr3:112615400-112617000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr3:112615400-112618400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr3:112616200-112617000	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr3:112616200-112617000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:112616200-112618400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:112616200-112622200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:112616400-112617000	Enhancers	Primary monocytes fromperipheralblood	blood

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