Variant report

Variant	rs12888097
Chromosome Location	chr14:56179309-56179310
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	chr14:55737454..55740283-chr14:56178729..56181502,2	MCF-7	breast:
2	chr14:56178438..56180249-chr14:56182200..56183742,2	K562	blood:

Variant related genes	Relation type
ENSG00000178974	Chromatin interaction
ENSG00000258413	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs17128719	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2342587	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832804	chr14:56083850-56277632	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv901966	chr14:56160904-56436203	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12888097	KTN1	cis	parietal	SCAN
rs12888097	GCH1	cis	cerebellum	SCAN
rs12888097	KTN1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
2	chr14:56154000-56191000	Weak transcription	Aorta	Aorta
3	chr14:56157600-56180000	Weak transcription	Primary B cells from cord blood	blood
4	chr14:56164600-56179600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr14:56169600-56182400	Weak transcription	GM12878-XiMat	blood
6	chr14:56170000-56182400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:56170400-56182400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:56172200-56182200	Weak transcription	HSMM	muscle
9	chr14:56172600-56182200	Weak transcription	HSMMtube	muscle
10	chr14:56174200-56182400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr14:56174600-56179600	Weak transcription	Brain Anterior Caudate	brain
12	chr14:56174600-56182400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:56178000-56180000	Enhancers	Psoas Muscle	Psoas
14	chr14:56178000-56182400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr14:56178000-56182400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:56178200-56179400	Weak transcription	Fetal Stomach	stomach
17	chr14:56178200-56183400	Weak transcription	Left Ventricle	heart
18	chr14:56178400-56181200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr14:56178400-56182400	Weak transcription	NHLF	lung
20	chr14:56178600-56180600	Enhancers	Placenta	Placenta
21	chr14:56179000-56179400	Enhancers	Brain Angular Gyrus	brain
22	chr14:56179000-56179800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr14:56179000-56180000	Enhancers	Liver	Liver
24	chr14:56179000-56180000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr14:56179000-56180000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr14:56179000-56181200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr14:56179200-56179800	Enhancers	Brain Cingulate Gyrus	brain
28	chr14:56179200-56179800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr14:56179200-56179800	Enhancers	Brain Substantia Nigra	brain
30	chr14:56179200-56180000	Enhancers	Brain Hippocampus Middle	brain

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