Variant report

Variant	rs12096661
Chromosome Location	chr1:210819646-210819647
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210811945..210813566-chr1:210817844..210819784,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12097792	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12736742	0.81[ASN][1000 genomes]
rs4951497	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][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	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv522480	chr1:210779936-210848344	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
3	esv1825229	chr1:210789477-210854976	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	n/a	inside rSNPs	diseases
4	nsv873150	chr1:210808270-210893233	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv873151	chr1:210818347-210846888	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12096661	NEK2	cis	parietal	SCAN
rs12096661	TRAF5	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210795400-210822600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:210801600-210823000	Weak transcription	Aorta	Aorta
3	chr1:210807800-210820400	Weak transcription	HSMM	muscle
4	chr1:210808600-210820400	Weak transcription	HSMMtube	muscle
5	chr1:210815200-210827000	Weak transcription	Pancreas	Pancrea
6	chr1:210818400-210821800	Enhancers	Fetal Stomach	stomach
7	chr1:210818600-210822200	Enhancers	HepG2	liver
8	chr1:210818800-210821800	Enhancers	Fetal Muscle Leg	muscle
9	chr1:210819000-210819800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:210819000-210820000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:210819000-210821000	Enhancers	Ovary	ovary
12	chr1:210819000-210822000	Enhancers	Fetal Lung	lung
13	chr1:210819200-210819800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:210819200-210820800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:210819400-210820200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:210819400-210820800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:210819400-210820800	Weak transcription	Left Ventricle	heart
18	chr1:210819400-210827000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:210819400-210827200	Weak transcription	Brain Anterior Caudate	brain
20	chr1:210819600-210820400	Weak transcription	Fetal Brain Female	brain
21	chr1:210819600-210820600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:210819600-210827200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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