Variant report

Variant	rs12084853
Chromosome Location	chr1:94155292-94155293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94144346..94147845-chr1:94153555..94157054,4	MCF-7	breast:
2	chr1:94150767..94155477-chr1:94157317..94159691,6	MCF-7	breast:
3	chr1:94146120..94150945-chr1:94154288..94160235,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1011903	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1011904	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11164961	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11164962	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11164963	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.93[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12057736	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12059154	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12079723	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12092517	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12568405	1.00[JPT][hapmap]
rs1567791	0.89[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1772781	1.00[JPT][hapmap]
rs236266	1.00[JPT][hapmap]
rs236284	0.87[CEU][hapmap]
rs236287	0.87[CEU][hapmap]
rs236295	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs236296	1.00[JPT][hapmap]
rs236308	0.90[JPT][hapmap]
rs236312	1.00[JPT][hapmap]
rs236313	1.00[JPT][hapmap]
rs236343	0.89[JPT][hapmap]
rs236344	0.86[MEX][hapmap]
rs3767979	0.89[JPT][hapmap]
rs3767991	1.00[JPT][hapmap]
rs399649	1.00[JPT][hapmap]
rs423493	1.00[JPT][hapmap]
rs61781002	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6541386	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6541387	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6541388	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6541389	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6656270	1.00[CEU][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6657709	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6660740	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6675484	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6684568	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6694536	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6701871	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6702036	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6704479	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7513130	0.85[CEU][hapmap]
rs7519952	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs798213	1.00[JPT][hapmap]
rs955470	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9659100	0.81[EUR][1000 genomes]

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	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12084853	F3	cis	cerebellum	SCAN
rs12084853	SNORD21	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94148200-94156800	Weak transcription	Adipose Nuclei	Adipose
2	chr1:94148200-94156800	Weak transcription	NHLF	lung
3	chr1:94148200-94167200	Weak transcription	Right Atrium	heart
4	chr1:94148400-94156200	Weak transcription	HSMM	muscle
5	chr1:94148400-94156600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:94148400-94156800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:94148800-94156400	Weak transcription	HMEC	breast
8	chr1:94150400-94156000	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:94152200-94155400	Weak transcription	Placenta	Placenta
10	chr1:94152200-94159000	Enhancers	Fetal Intestine Small	intestine
11	chr1:94152400-94157200	Weak transcription	Small Intestine	intestine
12	chr1:94152600-94155400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:94152600-94156400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:94152600-94156400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:94152600-94156800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:94152600-94156800	Weak transcription	Primary B cells from cord blood	blood
17	chr1:94152600-94157400	Weak transcription	HUVEC	blood vessel
18	chr1:94152800-94156600	Weak transcription	NHEK	skin
19	chr1:94153400-94156600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:94153600-94155400	Weak transcription	Hela-S3	cervix
21	chr1:94153800-94171600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:94154600-94155400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:94154600-94155400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:94154600-94155600	Enhancers	H9 Cell Line	embryonic stem cell
25	chr1:94154600-94155600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:94154600-94157600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:94154600-94159000	Enhancers	Duodenum Mucosa	Duodenum
28	chr1:94154800-94155400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:94155000-94157400	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:94155200-94155400	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:94155200-94155400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:94155200-94155400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:94155200-94155400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr1:94155200-94155400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:94155200-94155400	Enhancers	A549	lung
36	chr1:94155200-94155400	Enhancers	NH-A	brain
37	chr1:94155200-94155400	Enhancers	NHDF-Ad	bronchial
38	chr1:94155200-94155600	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr1:94155200-94155600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr1:94155200-94155600	Enhancers	Fetal Kidney	kidney
41	chr1:94155200-94155800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:94155200-94155800	Enhancers	GM12878-XiMat	blood
43	chr1:94155200-94156000	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr1:94155200-94157000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr1:94155200-94157400	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr1:94155200-94159400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:94155200-94159800	Enhancers	Fetal Intestine Large	intestine
48	chr1:94155200-94159800	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links