Variant report

Variant	rs10510820
Chromosome Location	chr3:59954385-59954386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1038516	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11130741	0.87[ASN][1000 genomes]
rs12486471	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12489929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12490525	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12490649	0.83[CEU][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17061712	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17253376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17254898	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17309998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17320834	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17374239	1.00[CHB][hapmap]
rs17375293	1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs212040	1.00[CHB][hapmap]
rs2366968	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3772446	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3772466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772470	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55649496	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55728186	0.87[ASN][1000 genomes]
rs55815123	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56045349	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56963766	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58197240	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60347439	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6786862	1.00[CHB][hapmap]
rs73089911	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73089917	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73089929	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73104585	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73104597	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73106507	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73106547	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73106565	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73106568	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931317	1.00[CHB][hapmap]
rs931321	1.00[CHB][hapmap]
rs9877140	1.00[CHB][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	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv876838	chr3:59952152-59999690	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59943200-59964400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:59943800-59959600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:59946400-59958200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:59948000-59957600	Weak transcription	Dnd41	blood
5	chr3:59952000-59961600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:59952000-59964400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:59954000-59955400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:59954000-59956200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr3:59954200-59954400	Enhancers	Brain Angular Gyrus	brain
10	chr3:59954200-59954600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:59954200-59954800	Enhancers	Fetal Brain Male	brain
12	chr3:59954200-59955000	Genic enhancers	Primary T cells from cord blood	blood
13	chr3:59954200-59955000	Enhancers	Cortex derived primary cultured neurospheres	brain

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