Variant report

Variant	rs3772468
Chromosome Location	chr3:59954966-59954967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10490808	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130742	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130743	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12630463	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13061330	0.88[ASN][1000 genomes]
rs13061337	0.81[EUR][1000 genomes]
rs13063413	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13070349	0.93[ASN][1000 genomes]
rs13070475	0.99[ASN][1000 genomes]
rs13073897	0.81[EUR][1000 genomes]
rs13077692	0.94[ASN][1000 genomes]
rs13081936	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13081972	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13088505	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13088669	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13092173	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13092997	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13094437	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13096138	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs212014	0.90[EUR][1000 genomes]
rs2687899	0.88[ASN][1000 genomes]
rs2736791	0.88[EUR][1000 genomes]
rs3772458	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3772464	0.82[ASN][1000 genomes]
rs3772473	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772483	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772484	0.99[ASN][1000 genomes]
rs3772491	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3772492	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3772499	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3772500	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3772502	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3772505	0.81[EUR][1000 genomes]
rs3821478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821479	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821480	0.93[ASN][1000 genomes]
rs3821481	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821482	0.93[ASN][1000 genomes]
rs6446101	0.85[EUR][1000 genomes]
rs6771484	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6771698	0.99[ASN][1000 genomes]
rs6784057	0.82[EUR][1000 genomes]
rs6805337	0.99[ASN][1000 genomes]
rs7615116	0.87[ASN][1000 genomes]
rs7640107	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs802772	0.93[ASN][1000 genomes]
rs802774	0.93[ASN][1000 genomes]
rs812445	0.93[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	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:15 , 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	chr3:59954200-59955000	Genic enhancers	Primary T cells from cord blood	blood
10	chr3:59954200-59955000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:59954400-59955000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr3:59954400-59955000	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:59954400-59956000	Enhancers	Fetal Brain Female	brain
14	chr3:59954800-59955200	Weak transcription	Fetal Brain Male	brain
15	chr3:59954800-59955400	Enhancers	Brain Anterior Caudate	brain

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