Variant report

Variant	rs12343629
Chromosome Location	chr9:116041581-116041582
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	chr9:116040629..116042415-chr9:116163599..116165929,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148218	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10117451	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10124515	0.81[CHB][hapmap]
rs10513189	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs10739390	0.87[CHB][hapmap]
rs10759636	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs10759637	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs10759638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817474	0.86[CEU][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10817475	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs10981710	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10981712	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10981715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10981720	0.81[EUR][1000 genomes]
rs10981762	0.81[CHB][hapmap]
rs11552582	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11789755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12236683	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12336832	0.91[YRI][hapmap]
rs12342197	0.95[YRI][hapmap]
rs12342549	0.95[YRI][hapmap]
rs12348629	0.96[YRI][hapmap]
rs2093691	0.86[CHB][hapmap]
rs2296073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3750532	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3750533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3750534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3750535	1.00[CEU][hapmap]
rs4560868	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs4979223	0.87[CHB][hapmap]
rs4979226	0.87[CHB][hapmap]
rs4979231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4979232	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.80[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4979233	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6477998	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs6478000	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6478006	0.81[CHB][hapmap]
rs7022397	0.86[CHB][hapmap]
rs7027833	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7041615	0.87[CHB][hapmap]
rs7847295	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7849326	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7849513	0.90[CHB][hapmap]
rs7850357	0.87[CHB][hapmap]
rs7851395	0.87[CHB][hapmap]
rs7860625	0.86[CHB][hapmap]
rs7868271	0.86[CHB][hapmap]
rs9299214	1.00[CEU][hapmap];0.80[CHB][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12343629	CDC26	cis	cerebellum	SCAN
rs12343629	CDC26	cis	Esophagus Muscularis	GTEx
rs12343629	CDC26	cis	lung	GTEx
rs12343629	CDC26	cis	Whole Blood	GTEx
rs12343629	CDC26	cis	Heart Left Ventricle	GTEx
rs12343629	CDC26	cis	parietal	SCAN
rs12343629	BSPRY	cis	Heart Left Ventricle	GTEx
rs12343629	ZNF618	cis	cerebellum	SCAN
rs12343629	PRPF4	cis	Thyroid	GTEx
rs12343629	CDC26	cis	Esophagus Mucosa	GTEx
rs12343629	CDC26	cis	Artery Tibial	GTEx
rs12343629	CDC26	cis	Muscle Skeletal	GTEx
rs12343629	CDC26	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116038600-116042200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:116038600-116050400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:116038800-116041800	Weak transcription	Fetal Kidney	kidney
4	chr9:116038800-116041800	Weak transcription	Small Intestine	intestine
5	chr9:116038800-116048400	Weak transcription	Stomach Mucosa	stomach
6	chr9:116038800-116060000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:116039000-116041800	Weak transcription	Psoas Muscle	Psoas
8	chr9:116039000-116041800	Weak transcription	Spleen	Spleen
9	chr9:116039000-116042000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:116039000-116042000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:116039000-116042000	Weak transcription	Brain Angular Gyrus	brain
12	chr9:116039000-116042000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:116039000-116042000	Weak transcription	Right Ventricle	heart
14	chr9:116039000-116042200	Weak transcription	Ovary	ovary
15	chr9:116039000-116042200	Weak transcription	Pancreas	Pancrea
16	chr9:116039000-116042200	Weak transcription	NHDF-Ad	bronchial
17	chr9:116039000-116043400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:116039000-116043400	Weak transcription	Colonic Mucosa	Colon
19	chr9:116039000-116056800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:116039000-116058200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:116039200-116049400	Strong transcription	Fetal Intestine Small	intestine
22	chr9:116039400-116051000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr9:116039400-116055200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:116039400-116055800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:116039400-116056200	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr9:116039400-116056400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:116039400-116056400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:116039400-116056400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr9:116039400-116056400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:116039400-116056600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr9:116039400-116056600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr9:116039400-116056600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr9:116039400-116056600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:116039400-116056600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:116039400-116056600	Strong transcription	Placenta	Placenta
36	chr9:116039400-116056600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:116039400-116056600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr9:116039400-116056800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:116039400-116056800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr9:116039600-116041800	Weak transcription	Primary T cells from cord blood	blood
41	chr9:116039600-116042000	Weak transcription	Fetal Heart	heart
42	chr9:116039600-116042200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr9:116039600-116055600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:116039600-116055800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
45	chr9:116039600-116056000	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr9:116039600-116056000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:116039600-116056200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr9:116039600-116056400	Strong transcription	Fetal Lung	lung
49	chr9:116039600-116056600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr9:116039600-116056800	Strong transcription	Primary monocytes fromperipheralblood	blood

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