Variant report

Variant	rs4971079
Chromosome Location	chr1:155130391-155130392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154955777..154957293-chr1:155130260..155131769,2	MCF-7	breast:
2	chr1:155112436..155115109-chr1:155129584..155132242,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179085	Chromatin interaction
ENSG00000160688	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1001848	0.85[JPT][hapmap]
rs10157801	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10908454	0.85[JPT][hapmap]
rs10908455	0.85[JPT][hapmap]
rs10908456	0.85[JPT][hapmap]
rs10908458	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264306	0.85[JPT][hapmap]
rs11264314	0.82[JPT][hapmap]
rs11264319	0.85[JPT][hapmap]
rs11264329	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs11264333	0.94[ASN][1000 genomes]
rs11264337	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11264338	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11264339	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11799962	1.00[ASN][1000 genomes]
rs12025371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12028043	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12040970	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs12124306	0.81[ASN][1000 genomes]
rs12127609	1.00[ASN][1000 genomes]
rs12145362	0.85[JPT][hapmap]
rs12752585	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1462855	0.85[JPT][hapmap]
rs1870939	0.85[JPT][hapmap]
rs2066981	0.83[CHB][hapmap];0.93[CHD][hapmap]
rs2306124	0.85[JPT][hapmap]
rs34257409	0.95[ASN][1000 genomes]
rs3765087	0.85[JPT][hapmap]
rs3766916	0.85[JPT][hapmap]
rs3814316	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4072037	0.84[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.80[YRI][hapmap]
rs4246529	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4276913	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4276914	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4390169	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4421576	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4460629	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4745	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4845407	0.85[JPT][hapmap]
rs4845408	0.85[JPT][hapmap]
rs4971052	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4971059	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs4971066	0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4971073	0.86[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4971076	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4971085	1.00[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971088	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971089	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4971100	0.81[CHD][hapmap]
rs6427158	0.85[JPT][hapmap]
rs6665822	0.80[GIH][hapmap];0.85[JPT][hapmap]
rs6676150	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6693477	0.85[JPT][hapmap]
rs7364524	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7365544	0.85[JPT][hapmap]
rs7367207	0.85[JPT][hapmap]
rs7367897	0.85[JPT][hapmap]
rs7368345	0.85[JPT][hapmap]
rs7534162	0.85[JPT][hapmap]
rs7548955	0.82[JPT][hapmap]
rs7556304	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs914615	0.84[CHB][hapmap];0.82[CHD][hapmap];0.86[YRI][hapmap]
rs9297	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv998756	chr1:155080090-155136545	Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
10	nsv946410	chr1:155119039-155135318	Bivalent Enhancer Enhancers Weak transcription	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs4971079	PRUNE	cis	cerebellum	SCAN
rs4971079	GBA	cis	lymphoblastoid	seeQTL
rs4971079	GBAP1	cis	Artery Tibial	GTEx
rs4971079	THEM5	cis	parietal	SCAN
rs4971079	RPRD2	cis	parietal	SCAN
rs4971079	LAMTOR2	cis	lymphoblastoid	seeQTL
rs4971079	GBA	cis	Esophagus Mucosa	GTEx
rs4971079	GBAP1	cis	Thyroid	GTEx
rs4971079	CRNN	cis	cerebellum	SCAN
rs4971079	TCHH	cis	cerebellum	SCAN
rs4971079	RP11-263K19.4	cis	Whole Blood	GTEx
rs4971079	IVL	cis	parietal	SCAN
rs4971079	THBS3	cis	Whole Blood	GTEx
rs4971079	SLC39A1	cis	parietal	SCAN
rs4971079	LASS2	cis	parietal	SCAN
rs4971079	ADAM15	cis	multi-tissue	Pritchard
rs4971079	GBAP1	cis	Adipose Subcutaneous	GTEx
rs4971079	CTR9	trans	brain	seeQTL
rs4971079	S100A3	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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