Variant report

Variant	rs820544
Chromosome Location	chr3:112406563-112406564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:112401424..112402927-chr3:112404953..112407128,2	K562	blood:
2	chr3:112396444..112398004-chr3:112404966..112407512,2	MCF-7	breast:
3	chr3:112404774..112406645-chr3:112438541..112440908,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11927615	0.80[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap]
rs1249910	0.91[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs1249929	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17457593	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2399449	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28374264	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3843366	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4145150	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4145151	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55894063	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56302621	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6768072	0.80[CEU][hapmap]
rs6772102	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6793555	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7630314	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs820545	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821100	0.91[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs9842816	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9845240	0.91[CEU][hapmap];0.80[CHB][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.84[EUR][1000 genomes]
rs9864580	0.81[AMR][1000 genomes]
rs9870933	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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 target site	39 gene(s)	inside rSNPs	diseases
2	nsv432477	chr3:112390310-112603310	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs820544	BOC	cis	cerebellum	SCAN
rs820544	ESAM	trans	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112391400-112407800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:112400400-112408200	Enhancers	NHLF	lung
3	chr3:112400600-112406600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:112400600-112408800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:112401000-112408800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:112401200-112413800	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:112401400-112408200	Enhancers	Osteobl	bone
8	chr3:112401600-112407000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:112401800-112407600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:112402600-112407800	Enhancers	NHDF-Ad	bronchial
11	chr3:112403000-112407400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:112403200-112407000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:112403200-112409200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:112403400-112407000	Weak transcription	HMEC	breast
15	chr3:112403400-112407000	Weak transcription	NHEK	skin
16	chr3:112403400-112409200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:112403600-112409600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:112404000-112409400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:112404200-112408600	Weak transcription	Primary T cells from cord blood	blood
20	chr3:112404200-112408800	Enhancers	NH-A	brain
21	chr3:112404400-112406800	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:112404400-112408200	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr3:112404400-112408800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:112404600-112406600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:112405200-112406600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:112405200-112409000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:112405200-112409200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:112405400-112406600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:112405400-112411800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:112405400-112412000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:112405800-112406800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:112405800-112411800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:112406000-112406800	Flanking Active TSS	A549	lung
34	chr3:112406000-112406800	Enhancers	K562	blood
35	chr3:112406000-112411800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:112406400-112408800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:112406400-112408800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links