Variant report

Variant	rs3020781
Chromosome Location	chr1:155269776-155269777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155260049..155265292-chr1:155266559..155270522,5	K562	blood:
2	chr1:155258950..155260585-chr1:155268243..155269943,2	MCF-7	breast:
3	chr1:155251831..155255812-chr1:155268570..155273078,4	K562	blood:
4	chr1:155263792..155265801-chr1:155268353..155270407,2	K562	blood:

Variant related genes	Relation type
ENSG00000143630	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10128085	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1046188	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1052176	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1052177	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1076556	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1078699	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10796941	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10796943	0.83[CHB][hapmap]
rs10796945	0.84[CHB][hapmap]
rs10908461	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10908462	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908463	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10908465	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs10908469	0.85[CHB][hapmap]
rs11264346	0.83[ASN][1000 genomes]
rs11264348	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264349	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11264352	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264353	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264354	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264355	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264357	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11264358	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264359	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11264361	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11264367	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs11264369	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs11264371	0.84[CHB][hapmap]
rs11264372	0.84[CHB][hapmap]
rs11264375	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs1142287	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11577338	0.85[ASN][1000 genomes]
rs12026638	0.90[CHB][hapmap]
rs12032720	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12041534	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs12042020	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12044063	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12049375	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12067675	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12079134	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs12239114	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs12563994	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12724079	0.84[CHB][hapmap]
rs12724449	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12749306	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1325908	0.84[CHB][hapmap]
rs1886905	0.80[CEU][hapmap]
rs2071053	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2075566	0.83[ASN][1000 genomes]
rs2236863	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2236864	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2242576	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2242577	0.83[ASN][1000 genomes]
rs2297480	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2361543	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34906309	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3762272	0.82[ASN][1000 genomes]
rs3814318	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3814319	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4620533	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971072	0.90[ASN][1000 genomes]
rs5005770	0.84[CEU][hapmap];0.84[CHB][hapmap]
rs6672284	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7520184	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7524950	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7534795	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7543234	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7549276	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7554780	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8177968	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8847	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs932972	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9426886	0.85[JPT][hapmap]
rs9729564	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
2	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
3	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
4	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
5	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
6	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
7	esv1832331	chr1:155213136-155271366	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
9	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
10	esv1826924	chr1:155230444-155271566	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	esv1832100	chr1:155230622-155269896	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
12	esv1827811	chr1:155230644-155271366	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	esv1827924	chr1:155230644-155271366	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
14	nsv872466	chr1:155259025-155269991	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3020781	GBA	cis	Esophagus Mucosa	GTEx
rs3020781	THBS3	cis	Whole Blood	GTEx
rs3020781	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs3020781	PKLR	cis	Nerve Tibial	GTEx
rs3020781	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs3020781	GBAP1	cis	Thyroid	GTEx
rs3020781	GBAP1	cis	Artery Tibial	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155265400-155277800	Weak transcription	Right Atrium	heart
2	chr1:155266800-155269800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:155267200-155270400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155267400-155271600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:155267800-155271400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:155267800-155276000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr1:155269200-155269800	Enhancers	Fetal Intestine Large	intestine
8	chr1:155269400-155269800	Enhancers	HepG2	liver
9	chr1:155269600-155269800	Flanking Active TSS	Liver	Liver
10	chr1:155269600-155269800	Enhancers	Fetal Intestine Small	intestine
11	chr1:155269600-155271000	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links