Variant report

Variant	rs4818045
Chromosome Location	chr21:40893224-40893225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40891710..40894102-chr21:40894328..40895948,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11088478	0.94[ASN][1000 genomes]
rs11701190	0.98[ASN][1000 genomes]
rs11701232	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11702769	0.98[ASN][1000 genomes]
rs12482418	0.97[ASN][1000 genomes]
rs13046275	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13050145	0.94[ASN][1000 genomes]
rs13051411	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1474384	0.98[ASN][1000 genomes]
rs1475593	0.96[ASN][1000 genomes]
rs1524929	0.99[ASN][1000 genomes]
rs2009713	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2026268	0.95[ASN][1000 genomes]
rs2037668	0.99[ASN][1000 genomes]
rs2178881	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2246616	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2837043	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837045	0.96[ASN][1000 genomes]
rs2837046	0.97[ASN][1000 genomes]
rs2837047	0.97[ASN][1000 genomes]
rs2837048	0.97[ASN][1000 genomes]
rs2837049	0.98[ASN][1000 genomes]
rs2837050	0.98[ASN][1000 genomes]
rs2837051	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837052	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837053	0.98[ASN][1000 genomes]
rs2837054	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837055	0.98[ASN][1000 genomes]
rs28634277	0.97[ASN][1000 genomes]
rs3787927	0.97[ASN][1000 genomes]
rs4118060	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4816629	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818038	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818039	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818040	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818041	0.98[ASN][1000 genomes]
rs4818042	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4818044	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818046	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517553	0.98[ASN][1000 genomes]
rs7277107	0.98[ASN][1000 genomes]
rs7278885	0.94[ASN][1000 genomes]
rs7280971	0.98[ASN][1000 genomes]
rs7281076	0.98[ASN][1000 genomes]
rs8126715	0.95[ASN][1000 genomes]
rs8126729	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8126860	0.98[ASN][1000 genomes]
rs8127748	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs8128567	0.98[ASN][1000 genomes]
rs8128795	0.98[ASN][1000 genomes]
rs8131355	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8132867	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8132996	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8133292	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8133862	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9974333	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9976202	0.98[ASN][1000 genomes]
rs9976208	0.98[ASN][1000 genomes]
rs9983297	0.97[ASN][1000 genomes]
rs9983428	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1062088	chr21:40838027-40919253	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv34779	chr21:40884871-40977473	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4818045	LCA5L	cis	Thyroid	GTEx
rs4818045	LCA5L	cis	Muscle Skeletal	GTEx
rs4818045	LCA5L	cis	Nerve Tibial	GTEx
rs4818045	LCA5L	cis	lung	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
2	chr21:40848200-40895600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr21:40875800-40895200	Weak transcription	Brain Substantia Nigra	brain
4	chr21:40875800-40898600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr21:40876400-40894600	Weak transcription	Gastric	stomach
6	chr21:40876400-40897400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr21:40877400-40899600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr21:40880200-40899800	Weak transcription	Fetal Muscle Leg	muscle
9	chr21:40887400-40895200	Weak transcription	Liver	Liver
10	chr21:40888000-40894800	Weak transcription	Aorta	Aorta
11	chr21:40888200-40895400	Weak transcription	Fetal Brain Male	brain
12	chr21:40888200-40907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr21:40888400-40895200	Weak transcription	Brain Anterior Caudate	brain
14	chr21:40890200-40897400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr21:40890800-40895200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr21:40890800-40895600	Weak transcription	Adipose Nuclei	Adipose
17	chr21:40891000-40895400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr21:40891000-40895400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr21:40891000-40895600	Weak transcription	Brain Hippocampus Middle	brain
20	chr21:40891200-40894800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr21:40891400-40894600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr21:40891600-40894400	Weak transcription	Pancreas	Pancrea
23	chr21:40891600-40894400	Weak transcription	Stomach Mucosa	stomach
24	chr21:40891600-40894800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr21:40891800-40893800	Weak transcription	Fetal Heart	heart
26	chr21:40891800-40894800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr21:40892000-40894600	Weak transcription	Left Ventricle	heart
28	chr21:40892000-40894800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr21:40892000-40894800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links