Variant report

Variant	rs12654454
Chromosome Location	chr5:178343791-178343792
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178338284..178340822-chr5:178341370..178344365,2	K562	blood:

Variant related genes	Relation type
ENSG00000198939	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10516152	0.83[JPT][hapmap]
rs11249600	0.92[JPT][hapmap]
rs11952817	0.92[JPT][hapmap]
rs12186577	0.89[CHB][hapmap]
rs12652691	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12653128	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12654612	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12654770	0.83[AMR][1000 genomes]
rs12654969	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12657931	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1566106	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs17078817	0.83[JPT][hapmap]
rs17078820	0.85[JPT][hapmap]
rs17078829	0.85[JPT][hapmap]
rs17078848	0.83[JPT][hapmap]
rs17078852	0.83[JPT][hapmap]
rs17078853	0.83[JPT][hapmap]
rs17078862	0.83[JPT][hapmap]
rs17078877	0.83[JPT][hapmap]
rs17078880	0.83[JPT][hapmap]
rs2645341	0.83[JPT][hapmap]
rs35030686	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3733915	0.83[JPT][hapmap]
rs59987112	0.83[AMR][1000 genomes]
rs61200088	0.83[AMR][1000 genomes]
rs62393041	0.82[ASN][1000 genomes]
rs62393043	0.82[ASN][1000 genomes]
rs62393044	0.82[ASN][1000 genomes]
rs62393045	0.82[ASN][1000 genomes]
rs7446382	0.82[ASN][1000 genomes]
rs7448421	0.91[JPT][hapmap]
rs7448445	0.91[JPT][hapmap]
rs7706632	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178335600-178349000	ZNF genes & repeats	Liver	Liver
2	chr5:178335800-178367000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr5:178340400-178344800	Weak transcription	Fetal Brain Male	brain
4	chr5:178340400-178345400	Weak transcription	Placenta	Placenta
5	chr5:178341600-178343800	ZNF genes & repeats	Aorta	Aorta
6	chr5:178341600-178345800	ZNF genes & repeats	Fetal Lung	lung
7	chr5:178341600-178345800	ZNF genes & repeats	Ovary	ovary
8	chr5:178341600-178347000	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr5:178341600-178347200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
10	chr5:178341600-178367000	ZNF genes & repeats	Fetal Brain Female	brain
11	chr5:178341800-178343800	ZNF genes & repeats	Pancreas	Pancrea
12	chr5:178342000-178348200	Weak transcription	Right Ventricle	heart
13	chr5:178342200-178345000	Weak transcription	Fetal Heart	heart
14	chr5:178342800-178343800	ZNF genes & repeats	Brain Angular Gyrus	brain
15	chr5:178342800-178343800	Strong transcription	Brain Germinal Matrix	brain
16	chr5:178342800-178343800	ZNF genes & repeats	Left Ventricle	heart
17	chr5:178342800-178343800	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:178342800-178344000	ZNF genes & repeats	Brain Cingulate Gyrus	brain
19	chr5:178342800-178346000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:178343000-178343800	ZNF genes & repeats	Brain Anterior Caudate	brain
21	chr5:178343000-178344000	ZNF genes & repeats	Brain Substantia Nigra	brain
22	chr5:178343000-178346000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
23	chr5:178343000-178367200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr5:178343200-178344000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:178343200-178344000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
26	chr5:178343400-178343800	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr5:178343400-178343800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:178343400-178344200	Weak transcription	Fetal Stomach	stomach
29	chr5:178343400-178345600	Weak transcription	Psoas Muscle	Psoas
30	chr5:178343600-178344000	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
31	chr5:178343600-178344200	ZNF genes & repeats	Fetal Kidney	kidney
32	chr5:178343600-178344800	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:178343600-178345000	Strong transcription	Brain Hippocampus Middle	brain

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