Variant report

Variant	rs2882467
Chromosome Location	chr12:29926776-29926777
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	chr12:29926045..29928762-chr12:29929311..29931905,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10743672	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743673	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10743674	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771578	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10771579	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10771580	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843501	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10843502	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10843503	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609828	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231167	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810794	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1551930	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs302335	1.00[ASW][hapmap];0.89[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.92[AMR][1000 genomes]
rs302336	0.92[AMR][1000 genomes]
rs302337	1.00[ASW][hapmap];0.89[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.92[AMR][1000 genomes]
rs302338	0.95[MEX][hapmap];0.92[AMR][1000 genomes]
rs4244848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244849	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931215	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931216	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4931217	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931218	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4931219	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56703053	0.81[AMR][1000 genomes]
rs67168837	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7967779	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][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	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv898953	chr12:29905322-29989292	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2882467	FGFR1OP2	cis	parietal	SCAN
rs2882467	TMTC1	cis	multi-tissue	Pritchard
rs2882467	FAR2	cis	lymphoblastoid	seeQTL
rs2882467	TMTC1	cis	Whole Blood	GTEx
rs2882467	FGD4	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29904200-29928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:29904600-29927800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:29906600-29928400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr12:29916000-29931400	Weak transcription	Pancreas	Pancrea
5	chr12:29919800-29927600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:29920400-29928400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:29921400-29927400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:29921600-29934000	Weak transcription	Fetal Kidney	kidney
9	chr12:29922600-29929600	Weak transcription	HSMM	muscle
10	chr12:29922600-29931000	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:29922600-29931800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:29922600-29934000	Weak transcription	NHLF	lung
13	chr12:29922800-29928200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:29922800-29928200	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:29922800-29930600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:29922800-29931200	Weak transcription	Aorta	Aorta
17	chr12:29922800-29933800	Weak transcription	Hela-S3	cervix
18	chr12:29924000-29926800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:29924200-29927800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:29924400-29927000	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr12:29924600-29931600	Weak transcription	Adipose Nuclei	Adipose
22	chr12:29925200-29928400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:29925400-29926800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:29925400-29927600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:29925400-29934000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:29925600-29926800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:29925600-29927400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:29925600-29927600	Weak transcription	NHDF-Ad	bronchial
29	chr12:29925600-29934200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:29925800-29927200	Enhancers	Fetal Heart	heart
31	chr12:29926000-29927000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:29926000-29927000	Enhancers	Left Ventricle	heart
33	chr12:29926000-29927200	Enhancers	Right Atrium	heart
34	chr12:29926000-29927200	Enhancers	Right Ventricle	heart
35	chr12:29926000-29928400	Enhancers	Psoas Muscle	Psoas
36	chr12:29926200-29928400	Weak transcription	HMEC	breast
37	chr12:29926400-29926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:29926400-29927200	Enhancers	Spleen	Spleen
39	chr12:29926400-29929200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:29926400-29931400	Weak transcription	Ovary	ovary
41	chr12:29926400-29931600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr12:29926600-29926800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr12:29926600-29927800	Weak transcription	Small Intestine	intestine
44	chr12:29926600-29931400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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