Variant report

Variant	rs17554034
Chromosome Location	chr6:53848551-53848552
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	chr6:53847388..53848999-chr6:53852029..53854591,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1409107	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1409108	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1610335	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17554130	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4142191	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55680514	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55696025	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55945235	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62396287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7742426	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759225	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357780	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758055	chr6:53839373-53996093	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv2759431	chr6:53839373-54007349	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1018062	chr6:53842588-53925192	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17554034	C6orf142	cis	cerebellum	SCAN
rs17554034	EFHC1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53846000-53850600	Weak transcription	Fetal Brain Male	brain
2	chr6:53846400-53852000	Enhancers	HMEC	breast
3	chr6:53846400-53852200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:53846600-53850200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:53846600-53850600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:53847000-53849200	Enhancers	Osteobl	bone
7	chr6:53847000-53849400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr6:53847000-53849400	Enhancers	NHEK	skin
9	chr6:53847000-53851800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:53847200-53848600	Enhancers	Psoas Muscle	Psoas
11	chr6:53847200-53849200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:53847200-53850600	Enhancers	HSMM	muscle
13	chr6:53847400-53849400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:53847400-53850400	Enhancers	NHDF-Ad	bronchial
15	chr6:53847600-53852200	Enhancers	NH-A	brain
16	chr6:53847800-53849200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:53847800-53849800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:53847800-53851000	Enhancers	Hela-S3	cervix
19	chr6:53848000-53849200	Weak transcription	HSMMtube	muscle
20	chr6:53848000-53849400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:53848200-53849200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:53848200-53850400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:53848400-53849200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:53848400-53849400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:53848400-53850600	Enhancers	NHLF	lung
26	chr6:53848400-53851800	Weak transcription	Right Ventricle	heart

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