Variant report

Variant	rs1263309
Chromosome Location	chr4:3051940-3051941
allele	C/T
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	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1313766	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313767	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313769	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1313770	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313772	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313773	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1313774	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2067003	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2471334	0.98[ASN][1000 genomes]
rs2798285	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2798289	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798296	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2798297	0.82[ASN][1000 genomes]
rs2857843	0.99[ASN][1000 genomes]
rs2857846	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857847	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857853	0.92[ASN][1000 genomes]
rs2857936	0.96[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3021126	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[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	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1263309	HTT-AS1	cis	Whole Blood	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3047400-3055600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:3048200-3075200	Weak transcription	Right Atrium	heart
3	chr4:3049600-3053600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:3049600-3074800	Weak transcription	Lung	lung
5	chr4:3049800-3056000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr4:3050600-3055400	Weak transcription	Primary B cells from cord blood	blood
7	chr4:3051000-3053400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:3051200-3052000	Enhancers	Osteobl	bone
9	chr4:3051800-3052400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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