Variant report

Variant	rs1421454
Chromosome Location	chr12:106349298-106349299
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	chr12:106348322..106349923-chr12:106353248..106355094,2	MCF-7	breast:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10507207	0.84[EUR][1000 genomes]
rs10861535	0.82[EUR][1000 genomes]
rs11112808	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11112810	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11112812	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112815	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608722	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11611601	0.85[EUR][1000 genomes]
rs11837217	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11837987	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12297788	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425164	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12426791	0.84[EUR][1000 genomes]
rs12426802	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12582103	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12810562	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12814823	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12815201	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12816747	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12818417	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12832619	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12833614	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1344566	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344567	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1345543	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1362980	0.84[EUR][1000 genomes]
rs1362981	0.84[EUR][1000 genomes]
rs1421456	0.81[AMR][1000 genomes]
rs1421457	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1421458	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1421459	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1895105	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1895106	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2032772	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2080755	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6539238	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6539239	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6539240	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6539241	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6539242	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7300069	0.84[EUR][1000 genomes]
rs7312545	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7953002	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7953243	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7955474	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7958273	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7960459	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961513	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7965501	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7969437	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971140	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971261	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7973513	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7973846	0.84[EUR][1000 genomes]
rs7976523	0.84[EUR][1000 genomes]
rs9630290	0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832508	chr12:106198797-106409112	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1421454	TCP11L2	cis	cerebellum	SCAN
rs1421454	CCDC53	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106340600-106355800	Weak transcription	Esophagus	oesophagus
2	chr12:106346200-106353800	Weak transcription	Lung	lung
3	chr12:106347400-106349600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:106347400-106349800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr12:106348200-106349600	Enhancers	Placenta	Placenta
6	chr12:106348200-106352000	Enhancers	Fetal Heart	heart
7	chr12:106348600-106349600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:106348600-106349600	Enhancers	Right Atrium	heart
9	chr12:106348600-106349600	Enhancers	NHEK	skin
10	chr12:106348600-106349800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:106348600-106349800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:106348600-106349800	Enhancers	HMEC	breast
13	chr12:106348600-106350000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:106348600-106350600	Enhancers	Right Ventricle	heart
15	chr12:106348800-106349400	Flanking Active TSS	K562	blood
16	chr12:106348800-106350400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:106348800-106350600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:106348800-106350800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:106348800-106351600	Enhancers	HSMMtube	muscle
20	chr12:106349000-106349400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:106349000-106349400	Weak transcription	Aorta	Aorta
22	chr12:106349000-106349600	Enhancers	Adipose Nuclei	Adipose
23	chr12:106349000-106349600	Enhancers	Fetal Intestine Small	intestine
24	chr12:106349000-106349800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:106349000-106350200	Weak transcription	Left Ventricle	heart
26	chr12:106349000-106350600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:106349200-106349600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:106349200-106349600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:106349200-106349600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:106349200-106349600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr12:106349200-106350200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:106349200-106350600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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