Variant report

Variant	rs1131671
Chromosome Location	chr2:133402607-133402608
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	chr2:133397006..133400489-chr2:133401960..133405775,6	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10179167	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10179785	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10189715	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13028563	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1430630	0.92[ASN][1000 genomes]
rs1430631	0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs1430632	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs17396523	0.92[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs17396537	0.92[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17396607	0.95[ASN][1000 genomes]
rs1897166	0.83[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2082179	0.89[ASN][1000 genomes]
rs2082181	0.85[ASN][1000 genomes]
rs2163342	0.92[ASN][1000 genomes]
rs2244888	0.89[ASN][1000 genomes]
rs2248193	0.88[ASN][1000 genomes]
rs2288653	0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs2315521	0.88[EUR][1000 genomes]
rs2315599	0.92[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2320153	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2435612	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2566528	0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2566529	0.84[ASN][1000 genomes]
rs2566530	0.80[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs2566535	0.86[ASN][1000 genomes]
rs2566536	0.86[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2566537	0.88[CEU][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs2566538	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2709520	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2709521	0.88[ASN][1000 genomes]
rs2709523	0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2709524	0.92[ASN][1000 genomes]
rs2709525	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2709526	0.94[ASN][1000 genomes]
rs2709527	0.92[ASN][1000 genomes]
rs2709528	0.91[ASN][1000 genomes]
rs2709532	0.87[ASN][1000 genomes]
rs2709533	0.85[ASN][1000 genomes]
rs2709545	0.80[ASN][1000 genomes]
rs2709546	0.80[ASN][1000 genomes]
rs2709548	0.83[CHD][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2709549	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs3738842	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4340582	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4547577	0.84[ASN][1000 genomes]
rs4547578	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4954351	0.92[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs4954352	0.92[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs6430370	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs713535	0.94[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs721470	0.87[ASN][1000 genomes]
rs744821	0.81[ASN][1000 genomes]
rs7558213	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558730	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7567602	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7603894	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7603926	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7608591	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9973717	0.92[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1131671	NCKAP5	cis	parietal	SCAN
rs1131671	LYPD1	cis	multi-tissue	Pritchard

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133389400-133403200	Weak transcription	Brain Anterior Caudate	brain
2	chr2:133390000-133403200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:133390200-133403200	Weak transcription	Esophagus	oesophagus
4	chr2:133390200-133412600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:133390400-133413800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:133390400-133423800	Weak transcription	A549	lung
7	chr2:133390800-133402800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:133390800-133405400	Weak transcription	Duodenum Mucosa	Duodenum
9	chr2:133396000-133403600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:133396200-133402800	Weak transcription	Gastric	stomach
11	chr2:133398600-133406000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:133398800-133402800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:133399000-133403200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:133399000-133403400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:133399000-133408800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:133399800-133410800	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:133400000-133403400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:133400200-133403200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:133400200-133405200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:133400400-133403800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:133401000-133403600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:133401000-133404400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:133401000-133404600	Strong transcription	NH-A	brain
24	chr2:133401200-133403200	Weak transcription	Fetal Intestine Large	intestine
25	chr2:133401400-133403800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:133402000-133403400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:133402000-133405800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:133402200-133404200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:133402200-133404800	Enhancers	Fetal Brain Female	brain
30	chr2:133402200-133406600	Weak transcription	HUVEC	blood vessel
31	chr2:133402600-133402800	Flanking Active TSS	Fetal Kidney	kidney
32	chr2:133402600-133403000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:133402600-133403000	Active TSS	Adipose Nuclei	Adipose
34	chr2:133402600-133403200	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:133402600-133403200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:133402600-133403200	Active TSS	Osteobl	bone
37	chr2:133402600-133403400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:133402600-133403400	Active TSS	Brain Germinal Matrix	brain
39	chr2:133402600-133403400	Strong transcription	Pancreas	Pancrea
40	chr2:133402600-133403800	Enhancers	Fetal Brain Male	brain
41	chr2:133402600-133404000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:133402600-133404000	Weak transcription	Fetal Heart	heart
43	chr2:133402600-133404000	Strong transcription	Fetal Stomach	stomach
44	chr2:133402600-133404200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:133402600-133404600	Strong transcription	Fetal Intestine Small	intestine

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