Variant report

Variant	rs1077842
Chromosome Location	chr1:48224582-48224583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3844086	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7543124	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[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	nsv829760	chr1:48111126-48308188	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv871257	chr1:48111699-48334490	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv871175	chr1:48150309-48254782	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1001126	chr1:48164622-48320862	Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1003161	chr1:48207715-48286563	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1077842	GPBP1L1	cis	cerebellum	SCAN
rs1077842	C1orf223	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:48215400-48236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:48216200-48226400	Weak transcription	Spleen	Spleen
3	chr1:48218600-48225200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:48218600-48228400	Weak transcription	Lung	lung
5	chr1:48218600-48239800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:48222000-48224600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr1:48222400-48231800	Weak transcription	Pancreas	Pancrea
8	chr1:48223200-48226600	Flanking Active TSS	Hela-S3	cervix
9	chr1:48223400-48225400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:48223800-48224600	Enhancers	Placenta	Placenta
11	chr1:48223800-48224800	Enhancers	Fetal Heart	heart
12	chr1:48223800-48225600	Enhancers	Fetal Intestine Large	intestine
13	chr1:48224000-48224600	Enhancers	Right Atrium	heart
14	chr1:48224000-48225600	Enhancers	Fetal Intestine Small	intestine
15	chr1:48224400-48228200	Weak transcription	Esophagus	oesophagus
16	chr1:48224400-48230400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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