Variant report

Variant	rs16832091
Chromosome Location	chr1:45045989-45045990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45045070..45047469-chr1:45047973..45050744,2	K562	blood:
2	chr1:45045070..45047329-chr1:45047973..45050362,2	K562	blood:
3	chr1:45044310..45046811-chr1:45054815..45057295,2	K562	blood:
4	chr1:45044706..45046382-chr1:45096271..45098129,2	MCF-7	breast:
5	chr1:45045874..45048149-chr1:45182908..45185522,3	K562	blood:
6	chr1:45043963..45046005-chr1:45050905..45053164,2	K562	blood:
7	chr1:45045874..45048115-chr1:45182908..45185522,2	K562	blood:

Variant related genes	Relation type
ENSG00000187147	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10158231	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11211015	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11581742	0.86[EUR][1000 genomes]
rs11591203	0.91[EUR][1000 genomes]
rs11807223	0.90[ASN][1000 genomes]
rs12119059	0.83[ASN][1000 genomes]
rs12127289	0.92[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12405833	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs12408210	0.81[EUR][1000 genomes]
rs12568345	0.92[JPT][hapmap]
rs12569316	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs156256	0.87[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs166589	0.83[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs172018	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs175222	0.87[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2355360	0.83[ASN][1000 genomes]
rs2378723	0.83[ASN][1000 genomes]
rs270715	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs270756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs270757	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs270767	0.82[EUR][1000 genomes]
rs270768	0.91[CEU][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes]
rs2924869	0.87[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs34090807	0.83[ASN][1000 genomes]
rs3738734	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850850	0.82[EUR][1000 genomes]
rs3850851	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3911861	0.92[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs56186608	0.84[ASN][1000 genomes]
rs59485926	0.91[ASN][1000 genomes]
rs61260531	0.99[ASN][1000 genomes]
rs61351118	0.84[ASN][1000 genomes]
rs6670379	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525212	0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs7553355	0.81[EUR][1000 genomes]
rs928685	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16832091	GUCA2A	cis	cerebellum	SCAN

Chromatin state (count:18 , 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	chr1:45040000-45047600	Enhancers	Brain Inferior Temporal Lobe	brain
5	chr1:45040200-45046400	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:45040200-45047400	Enhancers	Brain Anterior Caudate	brain
7	chr1:45042200-45048000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:45042200-45050600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:45042400-45051000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:45042600-45046400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:45043200-45046400	Weak transcription	Lung	lung
12	chr1:45043200-45051600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:45044200-45048200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:45044800-45046800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:45045000-45047000	Enhancers	Brain Angular Gyrus	brain
16	chr1:45045400-45046600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:45045600-45047800	Enhancers	Brain Substantia Nigra	brain
18	chr1:45045800-45046600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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