Variant report

Variant	rs2471334
Chromosome Location	chr4:3060049-3060050
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1263308	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263309	0.98[ASN][1000 genomes]
rs1313766	0.98[ASN][1000 genomes]
rs1313767	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1313769	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1313770	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313772	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313773	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1313774	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2067003	0.83[ASN][1000 genomes]
rs2798285	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2798289	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2798296	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798297	0.84[ASN][1000 genomes]
rs2857843	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857846	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2857847	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2857853	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2857936	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021126	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv13277	chr4:3059756-3069436	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2471334	HTT-AS1	cis	Whole Blood	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3048200-3075200	Weak transcription	Right Atrium	heart
2	chr4:3049600-3074800	Weak transcription	Lung	lung
3	chr4:3053800-3064600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:3058200-3060400	Weak transcription	Adipose Nuclei	Adipose
5	chr4:3058200-3075200	Weak transcription	Psoas Muscle	Psoas
6	chr4:3058400-3060200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:3058400-3060600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr4:3059200-3060400	Enhancers	Placenta	Placenta
9	chr4:3059600-3060200	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr4:3059600-3065200	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr4:3060000-3060200	Enhancers	GM12878-XiMat	blood
12	chr4:3060000-3060400	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr4:3060000-3060600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:3060000-3061400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr4:3060000-3061600	Enhancers	Primary B cells from cord blood	blood
16	chr4:3060000-3061600	Enhancers	Primary B cells from peripheral blood	blood
17	chr4:3060000-3061600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links