Variant report

Variant	rs6802964
Chromosome Location	chr3:112635194-112635195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12631307	0.95[ASN][1000 genomes]
rs12634138	0.83[ASN][1000 genomes]
rs12634629	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16860242	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs1919015	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306858	0.82[CHB][hapmap]
rs2399438	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3732813	0.82[CHB][hapmap]
rs3755743	0.82[CHB][hapmap]
rs3816832	0.82[CHB][hapmap]
rs4682121	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682123	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682124	0.82[AMR][1000 genomes]
rs4682438	1.00[CEU][hapmap]
rs4682439	0.81[EUR][1000 genomes]
rs4682446	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66732921	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66948543	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67184855	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770507	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6781132	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72950393	0.95[ASN][1000 genomes]
rs72950395	0.95[ASN][1000 genomes]
rs73227704	0.81[EUR][1000 genomes]
rs73227765	0.81[EUR][1000 genomes]
rs7634588	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7642984	0.86[YRI][hapmap]
rs9847757	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs9864286	1.00[CHB][hapmap];0.94[JPT][hapmap]

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	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
2	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
3	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
4	esv1843165	chr3:112628205-112740145	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6802964	C3orf17	cis	cerebellum	SCAN
rs6802964	SLC9A10	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112628000-112635200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:112628000-112641800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:112628000-112642000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:112628000-112642000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:112633400-112650800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:112634800-112635400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
7	chr3:112634800-112635600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
8	chr3:112634800-112635600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
9	chr3:112635000-112635600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
10	chr3:112635000-112635600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood

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