Variant report

Variant	rs69141
Chromosome Location	chr1:45039205-45039206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10890309	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs156651	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs156652	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs270706	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs270707	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes]
rs270708	0.96[CEU][hapmap];0.82[CHB][hapmap];0.86[EUR][1000 genomes]
rs270709	0.96[CEU][hapmap];0.82[CHB][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs270710	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs270711	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs270712	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs270713	0.87[EUR][1000 genomes]
rs270714	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs270760	0.92[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs270761	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs275075	0.89[CEU][hapmap]
rs61787550	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs69141	GPBP1L1	cis	cerebellum	SCAN
rs69141	LRRC41	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45018000-45082600	Weak transcription	Right Atrium	heart
2	chr1:45023800-45047600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:45029800-45047800	Enhancers	Brain Hippocampus Middle	brain
4	chr1:45031200-45040000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:45032200-45041000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr1:45032400-45042000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:45033400-45039800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:45034400-45039800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:45035400-45039800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:45036800-45044200	Enhancers	Brain Substantia Nigra	brain
11	chr1:45037600-45040200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:45038000-45039400	Weak transcription	Brain Anterior Caudate	brain
13	chr1:45038400-45040200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:45038400-45041400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:45038600-45040200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:45039000-45039600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:45039000-45041800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr1:45039200-45040000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:45039200-45040200	Weak transcription	Brain Angular Gyrus	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
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