Variant report

Variant	rs10179167
Chromosome Location	chr2:133400342-133400343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:133397006..133400489-chr2:133401960..133405775,6	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10179785	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10189715	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1131671	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13028563	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1430630	0.87[ASN][1000 genomes]
rs1430631	0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1430632	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs17396523	0.92[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs17396537	0.96[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17396607	0.90[ASN][1000 genomes]
rs1897166	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2082179	0.85[ASN][1000 genomes]
rs2082181	0.81[ASN][1000 genomes]
rs2163342	0.87[ASN][1000 genomes]
rs2244888	0.85[ASN][1000 genomes]
rs2248193	0.84[ASN][1000 genomes]
rs2288653	0.87[ASN][1000 genomes]
rs2315521	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2315599	0.96[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2320153	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2435612	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2566528	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2566535	0.82[ASN][1000 genomes]
rs2566536	0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2566537	0.92[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2566538	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2709520	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs2709521	0.84[ASN][1000 genomes]
rs2709523	0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2709524	0.87[ASN][1000 genomes]
rs2709525	0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2709526	0.90[ASN][1000 genomes]
rs2709527	0.87[ASN][1000 genomes]
rs2709528	0.87[ASN][1000 genomes]
rs2709532	0.83[ASN][1000 genomes]
rs2709533	0.81[ASN][1000 genomes]
rs2709548	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2709549	0.80[ASN][1000 genomes]
rs3738842	0.92[ASN][1000 genomes]
rs4340582	0.93[ASN][1000 genomes]
rs4547577	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4547578	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4954351	0.96[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4954352	0.96[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6430370	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs713535	0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs721470	0.83[ASN][1000 genomes]
rs7558213	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558730	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7567602	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7603894	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7603926	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608591	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs964842	0.82[YRI][hapmap]
rs9973717	0.96[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes];0.90[ASN][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	nsv1011421	chr2:132895241-133682185	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv875137	chr2:133167263-133714142	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1014306	chr2:133252736-133402581	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535925	chr2:133252736-133402581	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv583155	chr2:133253386-133415170	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv583158	chr2:133316092-133862100	Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10179167	NCKAP5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133389400-133403200	Weak transcription	Brain Anterior Caudate	brain
2	chr2:133390000-133401000	Weak transcription	NH-A	brain
3	chr2:133390000-133403200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:133390200-133403200	Weak transcription	Esophagus	oesophagus
5	chr2:133390200-133412600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:133390400-133402000	Weak transcription	Fetal Kidney	kidney
7	chr2:133390400-133413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:133390400-133423800	Weak transcription	A549	lung
9	chr2:133390800-133402800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:133390800-133405400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:133394600-133401000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:133394800-133401200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:133395400-133402600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:133395600-133402600	Weak transcription	Osteobl	bone
15	chr2:133396000-133403600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr2:133396200-133402800	Weak transcription	Gastric	stomach
17	chr2:133396400-133402600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:133396800-133402600	Weak transcription	Pancreas	Pancrea
19	chr2:133398400-133402600	Weak transcription	Fetal Stomach	stomach
20	chr2:133398600-133406000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:133398800-133400600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:133398800-133402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:133399000-133402200	Weak transcription	Fetal Brain Female	brain
24	chr2:133399000-133402600	Enhancers	Fetal Heart	heart
25	chr2:133399000-133403200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:133399000-133403400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:133399000-133408800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:133399200-133401200	Enhancers	Liver	Liver
29	chr2:133399400-133400600	Enhancers	Fetal Intestine Small	intestine
30	chr2:133399600-133400400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr2:133399600-133402200	Strong transcription	HUVEC	blood vessel
32	chr2:133399800-133400400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:133399800-133410800	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:133400000-133400400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:133400000-133401200	Enhancers	Fetal Intestine Large	intestine
36	chr2:133400000-133403400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:133400200-133400400	Enhancers	Fetal Brain Male	brain
38	chr2:133400200-133400600	Enhancers	HepG2	liver
39	chr2:133400200-133403200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:133400200-133405200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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