Variant report

Variant	rs1008040
Chromosome Location	chr12:42901825-42901826
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	chr12:42896669..42898577-chr12:42900249..42903063,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10785343	0.98[ASN][1000 genomes]
rs10880309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880311	0.95[ASN][1000 genomes]
rs12424992	0.98[ASN][1000 genomes]
rs12822031	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1985217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019557	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406678	0.99[ASN][1000 genomes]
rs2406680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2406681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2406682	0.98[ASN][1000 genomes]
rs28491015	0.99[ASN][1000 genomes]
rs28689646	0.95[ASN][1000 genomes]
rs3895894	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307491	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669495	0.98[ASN][1000 genomes]

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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42878600-42904800	Weak transcription	Right Atrium	heart
2	chr12:42878800-42902000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr12:42885400-42913600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:42886800-42904800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:42889800-42902800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:42890600-42905800	Weak transcription	Osteobl	bone
7	chr12:42891000-42910200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:42898400-42914000	Weak transcription	NH-A	brain
9	chr12:42898400-42929000	Weak transcription	Fetal Kidney	kidney
10	chr12:42898600-42902400	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:42898600-42904400	Weak transcription	HUVEC	blood vessel
12	chr12:42898600-42910400	Weak transcription	Fetal Stomach	stomach
13	chr12:42899000-42910000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:42900600-42902000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr12:42900600-42903400	Enhancers	Fetal Heart	heart
16	chr12:42901200-42902800	Weak transcription	HSMMtube	muscle
17	chr12:42901200-42903000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:42901200-42905800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:42901400-42902400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:42901400-42905200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:42901600-42902600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:42901600-42902600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:42901600-42904600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:42901600-42904600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:42901600-42940200	Weak transcription	Ovary	ovary

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