Variant report

Variant	rs12141555
Chromosome Location	chr1:171227487-171227488
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	chr1:171223210..171225976-chr1:171227419..171229692,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10399602	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10399952	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10798297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912672	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912673	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912713	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10912714	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10912723	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10912736	0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1126692	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11484641	0.82[AMR][1000 genomes]
rs11484642	0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11487396	0.89[AMR][1000 genomes]
rs12057955	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12058402	0.98[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12059179	0.89[AMR][1000 genomes]
rs12062692	0.94[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12068552	0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12070766	0.89[AMR][1000 genomes]
rs12072043	0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12077231	0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12077755	0.89[AMR][1000 genomes]
rs12079141	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12080449	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12081291	0.89[AMR][1000 genomes]
rs12091482	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12092985	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12094878	0.98[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12354390	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12726624	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12729885	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12730181	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12742008	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12745080	0.89[AMR][1000 genomes]
rs12747080	0.89[AMR][1000 genomes]
rs12757839	0.86[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13376631	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864302	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16864387	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17581251	1.00[ASN][1000 genomes]
rs2006986	0.89[AMR][1000 genomes]
rs2076322	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2092311	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes]
rs2284131	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs28741369	0.94[ASN][1000 genomes]
rs34118031	0.94[ASN][1000 genomes]
rs34320519	0.94[ASN][1000 genomes]
rs4607925	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs55949630	0.89[AMR][1000 genomes]
rs6670639	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6674596	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs742350	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs742351	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7512853	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7519999	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7539057	0.83[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7541377	0.89[AMR][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12141555	FMO4	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171221000-171227600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:171221200-171228200	Enhancers	Fetal Intestine Large	intestine
3	chr1:171224800-171227800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr1:171225000-171227600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:171225000-171228000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:171226000-171228000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:171226000-171228600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:171226000-171228800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:171226000-171228800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:171226000-171228800	Enhancers	NHEK	skin
11	chr1:171226000-171229200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:171226200-171227800	Enhancers	Fetal Heart	heart
13	chr1:171226200-171228800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr1:171226200-171229200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:171226400-171228200	Enhancers	Fetal Stomach	stomach
16	chr1:171226400-171228600	Enhancers	Adipose Nuclei	Adipose
17	chr1:171226400-171229200	Enhancers	Ovary	ovary
18	chr1:171226600-171228200	Flanking Active TSS	Fetal Muscle Trunk	muscle
19	chr1:171226600-171228600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:171226600-171229200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:171226600-171229200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:171226800-171227800	Weak transcription	Right Atrium	heart
23	chr1:171226800-171228000	Weak transcription	Fetal Kidney	kidney
24	chr1:171226800-171228200	Active TSS	Stomach Smooth Muscle	stomach
25	chr1:171226800-171228600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr1:171226800-171228800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:171227000-171227600	Weak transcription	Fetal Thymus	thymus
28	chr1:171227000-171227800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:171227200-171227600	Weak transcription	Placenta	Placenta
30	chr1:171227200-171228200	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr1:171227200-171228200	Weak transcription	HMEC	breast
32	chr1:171227200-171228600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:171227200-171228600	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr1:171227200-171228600	Genic enhancers	Fetal Intestine Small	intestine
35	chr1:171227200-171228600	Enhancers	Fetal Lung	lung
36	chr1:171227200-171229000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr1:171227400-171227600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:171227400-171228200	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr1:171227400-171228600	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr1:171227400-171229000	Enhancers	HUES48 Cell Line	embryonic stem cell

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