Variant report

Variant	rs12434554
Chromosome Location	chr14:56174105-56174106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:56173843..56174384-chr14:56948949..56949696,2	MCF-7	breast:
2	chr14:56172874..56174577-chr14:56174772..56176710,2	MCF-7	breast:
3	chr14:55890007..55892259-chr14:56172820..56174391,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10444721	0.90[JPT][hapmap]
rs10483644	0.90[JPT][hapmap]
rs12432344	0.82[AMR][1000 genomes]
rs12432887	0.90[JPT][hapmap]
rs12435643	0.90[JPT][hapmap]
rs12587735	0.90[JPT][hapmap]
rs12590388	0.90[JPT][hapmap]
rs12590936	0.90[JPT][hapmap]
rs12888809	0.94[JPT][hapmap]
rs12893162	0.85[JPT][hapmap]
rs12895072	0.97[ASN][1000 genomes]
rs17128657	0.90[JPT][hapmap]
rs17128684	0.90[JPT][hapmap]
rs1951887	0.90[JPT][hapmap]
rs1951889	0.90[JPT][hapmap]
rs2252189	0.90[JPT][hapmap]
rs2274076	0.89[JPT][hapmap]
rs2274078	0.89[JPT][hapmap]
rs2296182	0.89[JPT][hapmap]
rs3765515	0.90[JPT][hapmap]
rs6573053	0.90[JPT][hapmap]
rs6573054	0.90[JPT][hapmap]
rs7156566	0.90[JPT][hapmap]

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
rs12434554	KTN1	cis	cerebellum	SCAN
rs12434554	GCH1	cis	cerebellum	SCAN
rs12434554	KTN1	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56102400-56185400	Weak transcription	Right Ventricle	heart
2	chr14:56154000-56177800	Weak transcription	Left Ventricle	heart
3	chr14:56154000-56191000	Weak transcription	Aorta	Aorta
4	chr14:56154400-56177800	Weak transcription	Fetal Muscle Leg	muscle
5	chr14:56157600-56178000	Weak transcription	Psoas Muscle	Psoas
6	chr14:56157600-56180000	Weak transcription	Primary B cells from cord blood	blood
7	chr14:56164600-56179600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:56168600-56174600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr14:56169000-56177400	Weak transcription	Osteobl	bone
10	chr14:56169600-56182400	Weak transcription	GM12878-XiMat	blood
11	chr14:56170000-56182400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr14:56170400-56182400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr14:56170800-56177800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr14:56171800-56175000	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr14:56172000-56174600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr14:56172200-56174200	Enhancers	Fetal Thymus	thymus
17	chr14:56172200-56174600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr14:56172200-56182200	Weak transcription	HSMM	muscle
19	chr14:56172600-56182200	Weak transcription	HSMMtube	muscle
20	chr14:56172800-56174400	Enhancers	A549	lung
21	chr14:56173600-56174600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr14:56173600-56174600	Enhancers	NHLF	lung
23	chr14:56173800-56174200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr14:56173800-56174200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr14:56173800-56174800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr14:56174000-56174200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr14:56174000-56174200	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr14:56174000-56174200	Enhancers	NHDF-Ad	bronchial
29	chr14:56174000-56174400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr14:56174000-56174600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr14:56174000-56174600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr14:56174000-56174600	Enhancers	Brain Angular Gyrus	brain
33	chr14:56174000-56174600	Enhancers	Brain Anterior Caudate	brain
34	chr14:56174000-56174600	Enhancers	Brain Cingulate Gyrus	brain
35	chr14:56174000-56174600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr14:56174000-56177400	Weak transcription	Right Atrium	heart

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