Variant report

Variant	rs1389484
Chromosome Location	chr12:76203505-76203506
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	chr12:76016288..76017848-chr12:76202923..76204830,2	MCF-7	breast:

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10748289	0.81[CEU][hapmap]
rs10748290	0.81[CEU][hapmap]
rs10879987	0.82[CEU][hapmap]
rs11611462	0.82[CEU][hapmap]
rs1275555	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv832463	chr12:76136551-76316703	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv899315	chr12:76163309-76385096	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1041730	chr12:76198863-76331900	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1389484	CAPS2	cis	cerebellum	SCAN
rs1389484	LOC283392	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76198000-76205000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:76199800-76205800	Weak transcription	NHDF-Ad	bronchial
3	chr12:76202600-76203800	Enhancers	NHEK	skin
4	chr12:76202600-76208000	Enhancers	Fetal Brain Male	brain
5	chr12:76202800-76203800	Enhancers	Fetal Heart	heart
6	chr12:76202800-76204200	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr12:76202800-76204400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:76202800-76206000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:76203000-76203600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:76203000-76203800	Enhancers	HMEC	breast
11	chr12:76203000-76204000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr12:76203000-76204000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:76203000-76204200	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr12:76203000-76204400	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr12:76203000-76204400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:76203000-76204600	Enhancers	H9 Cell Line	embryonic stem cell
17	chr12:76203000-76204800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr12:76203000-76205800	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr12:76203000-76206000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:76203000-76210400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:76203200-76203600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:76203200-76204000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr12:76203200-76204200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr12:76203200-76204400	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr12:76203200-76206800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:76203400-76204000	Enhancers	Brain Germinal Matrix	brain
27	chr12:76203400-76208800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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