Variant report

Variant	rs2819531
Chromosome Location	chr1:172106197-172106198
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	chr1:172095415..172097843-chr1:172105247..172107080,2	MCF-7	breast:
2	chr1:172101341..172102899-chr1:172105210..172106903,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGC-1	chr1:172106019-172113975	NONHSAT007596
2	lnc-PIGC-1	chr1:172106019-172109736	NONHSAT007597

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10752861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10911275	0.82[CEU][hapmap]
rs12090953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2761184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761185	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2761186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2761187	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2761190	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28378748	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4244191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4641331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4916242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4916418	0.90[CHB][hapmap]
rs6425637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425638	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6665598	1.00[CEU][hapmap];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172049400-172110800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:172062400-172109200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:172077200-172110600	Weak transcription	Brain Angular Gyrus	brain
4	chr1:172085800-172113400	Weak transcription	Pancreas	Pancrea
5	chr1:172090000-172109600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:172090400-172108800	Weak transcription	Fetal Stomach	stomach
7	chr1:172094600-172110600	Weak transcription	Left Ventricle	heart
8	chr1:172096400-172110600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:172100200-172108600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:172101200-172107800	Weak transcription	Psoas Muscle	Psoas
11	chr1:172102000-172113400	Weak transcription	Lung	lung
12	chr1:172102600-172113400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:172102600-172113600	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:172103200-172110400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:172103400-172107800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:172103800-172106200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:172103800-172108000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:172103800-172109200	Weak transcription	Brain Anterior Caudate	brain
19	chr1:172104000-172107600	Weak transcription	HMEC	breast
20	chr1:172104000-172107800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr1:172104200-172107600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:172104200-172107600	Weak transcription	NHEK	skin
23	chr1:172104400-172106400	Enhancers	HUVEC	blood vessel
24	chr1:172104400-172107400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:172104400-172107800	Weak transcription	Ovary	ovary
26	chr1:172104800-172106200	Enhancers	NH-A	brain
27	chr1:172105000-172106400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr1:172105200-172106200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:172105200-172106200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:172105400-172106400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:172105400-172106400	Enhancers	Fetal Lung	lung
32	chr1:172105400-172106600	Enhancers	HSMM	muscle
33	chr1:172105400-172106600	Enhancers	NHLF	lung
34	chr1:172105400-172109600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:172105800-172106200	Enhancers	NHDF-Ad	bronchial
36	chr1:172106000-172106200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:172106000-172106200	Enhancers	Adipose Nuclei	Adipose
38	chr1:172106000-172106400	Enhancers	Fetal Muscle Leg	muscle
39	chr1:172106000-172106400	Enhancers	Right Atrium	heart
40	chr1:172106000-172106400	Flanking Active TSS	Osteobl	bone
41	chr1:172106000-172106600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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