Variant report

Variant	rs4970980
Chromosome Location	chr1:150864992-150864993
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150847751..150849634-chr1:150864149..150866867,2	MCF-7	breast:
2	chr1:150533054..150535535-chr1:150864232..150866971,2	MCF-7	breast:
3	chr1:150863507..150866483-chr1:151030495..151033374,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143437	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000203804	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1027699	0.86[EUR][1000 genomes]
rs10305664	0.86[EUR][1000 genomes]
rs10305672	0.84[EUR][1000 genomes]
rs10305673	0.86[EUR][1000 genomes]
rs10305704	0.86[EUR][1000 genomes]
rs10305711	0.86[EUR][1000 genomes]
rs10305714	0.86[EUR][1000 genomes]
rs10305720	0.89[EUR][1000 genomes]
rs10399947	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10788794	0.82[EUR][1000 genomes]
rs10888391	0.82[EUR][1000 genomes]
rs10888392	0.83[EUR][1000 genomes]
rs10888394	0.85[EUR][1000 genomes]
rs10888395	0.87[EUR][1000 genomes]
rs10888397	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888398	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204722	0.82[EUR][1000 genomes]
rs11204726	0.85[EUR][1000 genomes]
rs11204733	0.85[EUR][1000 genomes]
rs11204739	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204742	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204743	0.90[ASN][1000 genomes]
rs11204747	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204748	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204749	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204750	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11552229	0.86[EUR][1000 genomes]
rs11581757	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11582281	0.85[EUR][1000 genomes]
rs11589458	0.86[EUR][1000 genomes]
rs11589886	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11800855	0.94[EUR][1000 genomes]
rs12059949	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12075597	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12085336	0.93[EUR][1000 genomes]
rs12090215	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12096831	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12097963	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12409208	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12410394	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12410869	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1532770	0.81[EUR][1000 genomes]
rs1546376	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16827671	0.85[EUR][1000 genomes]
rs17660092	0.86[EUR][1000 genomes]
rs1889740	0.94[EUR][1000 genomes]
rs1889741	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1972060	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2004903	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2089082	0.86[EUR][1000 genomes]
rs2124952	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2228099	0.94[EUR][1000 genomes]
rs2256355	0.94[EUR][1000 genomes]
rs2271076	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2272214	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280627	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2864873	0.94[EUR][1000 genomes]
rs2864882	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2867296	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2867297	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34985895	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36008098	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3768013	0.93[EUR][1000 genomes]
rs3768015	0.86[EUR][1000 genomes]
rs3768016	0.86[EUR][1000 genomes]
rs3768018	0.82[EUR][1000 genomes]
rs3843843	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3849279	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4451553	0.88[ASN][1000 genomes]
rs4970928	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4970929	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4970930	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4970931	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970982	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4970984	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970985	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970986	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59024312	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59337856	0.85[EUR][1000 genomes]
rs6587542	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6658066	0.89[ASN][1000 genomes]
rs6660084	0.85[EUR][1000 genomes]
rs6660845	0.89[EUR][1000 genomes]
rs6669855	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6677420	0.81[ASN][1000 genomes]
rs66847267	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6686064	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72704639	0.80[EUR][1000 genomes]
rs72704652	0.86[EUR][1000 genomes]
rs72704654	0.86[EUR][1000 genomes]
rs72704656	0.94[EUR][1000 genomes]
rs72704658	0.86[EUR][1000 genomes]
rs72704679	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72704682	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72704685	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7514004	0.94[EUR][1000 genomes]
rs7518156	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7521592	0.86[EUR][1000 genomes]
rs752376	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7528773	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7532045	0.93[EUR][1000 genomes]
rs7556451	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7556661	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8444	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs897815	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9661876	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv2810	chr1:150835173-150879869	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs4970980	HORMAD1	cis	Esophagus Mucosa	GTEx
rs4970980	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs4970980	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs4970980	RP11-316M1.12	cis	lung	GTEx
rs4970980	RP11-316M1.12	cis	Artery Aorta	GTEx
rs4970980	RP11-316M1.12	cis	Artery Tibial	GTEx
rs4970980	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs4970980	CTSS	cis	Thyroid	GTEx
rs4970980	RP11-316M1.12	cis	Whole Blood	GTEx
rs4970980	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs4970980	CTSS	cis	multi-tissue	Pritchard
rs4970980	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs4970980	RP11-316M1.12	cis	Skin Sun Exposed Lower leg	GTEx
rs4970980	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs4970980	RP11-316M1.12	cis	Thyroid	GTEx
rs4970980	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs4970980	RP11-316M1.12	cis	Muscle Skeletal	GTEx
rs4970980	RP11-98D18.3	cis	Esophagus Mucosa	GTEx
rs4970980	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs4970980	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs4970980	HORMAD1	cis	Nerve Tibial	GTEx
rs4970980	RP11-316M1.12	cis	Esophagus Mucosa	GTEx
rs4970980	GOLPH3L	cis	Nerve Tibial	GTEx
rs4970980	RP11-316M1.12	cis	Heart Left Ventricle	GTEx
rs4970980	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150859800-150867800	Weak transcription	Hela-S3	cervix
2	chr1:150863600-150866600	Enhancers	Placenta	Placenta
3	chr1:150864000-150865000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:150864800-150865000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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