Variant report

Variant	rs4971072
Chromosome Location	chr1:155273869-155273870
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155242743..155244954-chr1:155272841..155275388,3	K562	blood:
2	chr1:155270303..155273300-chr1:155273424..155278245,4	MCF-7	breast:
3	chr1:155254134..155256609-chr1:155273480..155276250,2	MCF-7	breast:
4	chr1:155242743..155244503-chr1:155272841..155275388,2	K562	blood:
5	chr1:155187979..155190547-chr1:155272522..155275143,2	K562	blood:
6	chr1:155258490..155260000-chr1:155271609..155274167,2	K562	blood:
7	chr1:155241917..155244553-chr1:155272889..155274441,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143627	Chromatin interaction
ENSG00000176444	Chromatin interaction
ENSG00000160766	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1052176	0.83[ASN][1000 genomes]
rs1052177	0.83[ASN][1000 genomes]
rs10796941	0.85[ASN][1000 genomes]
rs10796943	0.82[CHB][hapmap]
rs10796945	0.84[CHB][hapmap]
rs10908461	0.99[ASN][1000 genomes]
rs10908463	0.84[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs10908465	0.84[CHB][hapmap]
rs10908469	0.84[CHB][hapmap]
rs11264355	0.88[ASN][1000 genomes]
rs11264358	0.98[ASN][1000 genomes]
rs11264359	0.90[CHB][hapmap];0.84[CHD][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs11264361	0.84[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs11264363	0.89[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs11264367	0.84[CHB][hapmap]
rs11264369	0.84[CHB][hapmap]
rs11264371	0.84[CHB][hapmap]
rs11264372	0.84[CHB][hapmap]
rs11264375	0.84[CHB][hapmap]
rs11577338	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12026638	0.89[CHB][hapmap]
rs12032720	0.99[ASN][1000 genomes]
rs12041534	0.84[CHB][hapmap]
rs12049375	0.81[ASN][1000 genomes]
rs12067675	0.81[ASN][1000 genomes]
rs12079134	0.84[CHB][hapmap]
rs12239114	0.84[CHB][hapmap]
rs12724079	0.89[CEU][hapmap];0.84[CHB][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs1325908	0.84[CHB][hapmap];0.86[MEX][hapmap]
rs1360554	0.85[CEU][hapmap];0.84[CHB][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs1886905	0.86[MEX][hapmap]
rs2071053	0.83[ASN][1000 genomes]
rs2297480	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3020781	0.90[ASN][1000 genomes]
rs3814318	0.83[ASN][1000 genomes]
rs3814319	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4620533	0.83[ASN][1000 genomes]
rs5005770	0.84[CHB][hapmap]
rs6672284	0.98[ASN][1000 genomes]
rs6684889	0.88[CEU][hapmap]
rs7520184	0.81[ASN][1000 genomes]
rs7524950	0.91[ASN][1000 genomes]
rs7534795	0.99[ASN][1000 genomes]
rs7556102	0.85[CEU][hapmap]
rs8177968	0.81[ASN][1000 genomes]
rs8847	0.83[ASN][1000 genomes]
rs932972	0.83[ASN][1000 genomes]
rs9426886	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
8	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4971072	GBA	cis	Esophagus Mucosa	GTEx
rs4971072	GBAP1	cis	Artery Tibial	GTEx
rs4971072	YY1AP1	cis	cerebellum	SCAN
rs4971072	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs4971072	HDGF	cis	parietal	SCAN
rs4971072	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs4971072	THEM5	cis	parietal	SCAN
rs4971072	BCAN	cis	cerebellum	SCAN
rs4971072	PRUNE	cis	cerebellum	SCAN
rs4971072	THBS3	cis	Whole Blood	GTEx
rs4971072	CRNN	cis	cerebellum	SCAN
rs4971072	S100A8	cis	cerebellum	SCAN
rs4971072	GBAP1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155265400-155277800	Weak transcription	Right Atrium	heart
2	chr1:155267800-155276000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:155270600-155275800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155270800-155274200	Weak transcription	Colonic Mucosa	Colon
5	chr1:155270800-155278600	Weak transcription	Small Intestine	intestine
6	chr1:155271200-155274400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:155271200-155274400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:155271400-155274400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr1:155271400-155274400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:155271800-155274400	Weak transcription	Fetal Intestine Small	intestine
11	chr1:155271800-155275800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:155271800-155276000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:155271800-155276800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:155271800-155277400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:155272000-155274400	Weak transcription	Fetal Intestine Large	intestine
16	chr1:155272600-155274200	Enhancers	HepG2	liver
17	chr1:155272600-155277800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:155273000-155275200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:155273200-155274600	Weak transcription	K562	blood
20	chr1:155273800-155274000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:155273800-155274200	Enhancers	Liver	Liver

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