Variant report

Variant	rs6865775
Chromosome Location	chr5:178069708-178069709
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178063343..178066239-chr5:178068092..178071855,3	K562	blood:
2	chr5:178068786..178070485-chr5:178285639..178288443,2	MCF-7	breast:
3	chr5:178068917..178070441-chr5:178081330..178082973,2	MCF-7	breast:
4	chr5:178063122..178065248-chr5:178068092..178070072,3	K562	blood:
5	chr5:178053031..178055568-chr5:178069602..178071644,2	MCF-7	breast:
6	chr5:178060070..178062652-chr5:178068693..178071518,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178338	Chromatin interaction
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10063220	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249556	0.82[ASN][1000 genomes]
rs11737903	0.83[ASN][1000 genomes]
rs11740194	0.83[ASN][1000 genomes]
rs11746942	0.83[ASN][1000 genomes]
rs11747742	0.83[ASN][1000 genomes]
rs12514311	0.85[ASN][1000 genomes]
rs12518589	0.91[ASN][1000 genomes]
rs13156622	0.89[ASN][1000 genomes]
rs35522922	0.89[ASN][1000 genomes]
rs36008351	0.91[ASN][1000 genomes]
rs3925518	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4079110	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4587090	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4976738	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4976800	0.82[ASN][1000 genomes]
rs530542	0.82[ASN][1000 genomes]
rs643936	0.83[ASN][1000 genomes]
rs6863876	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6882079	0.83[ASN][1000 genomes]
rs6883747	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890632	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702727	0.83[ASN][1000 genomes]
rs9329045	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9329046	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6865775	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178067400-178070400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:178067400-178070800	Enhancers	HMEC	breast
3	chr5:178067600-178070200	Enhancers	NHDF-Ad	bronchial
4	chr5:178067600-178070800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:178067600-178072400	Enhancers	Osteobl	bone
6	chr5:178068000-178070200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr5:178068600-178070400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:178068800-178069800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:178068800-178070600	Enhancers	HUVEC	blood vessel
10	chr5:178068800-178070600	Enhancers	NH-A	brain
11	chr5:178069000-178070000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:178069000-178070200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:178069000-178070200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:178069000-178070200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:178069200-178070000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:178069200-178070000	Enhancers	Esophagus	oesophagus
17	chr5:178069200-178070400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr5:178069400-178070000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:178069400-178070000	Enhancers	Placenta	Placenta
20	chr5:178069400-178070200	Enhancers	NHEK	skin
21	chr5:178069400-178070400	Enhancers	Hela-S3	cervix
22	chr5:178069600-178070000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr5:178069600-178070000	Enhancers	Pancreas	Pancrea
24	chr5:178069600-178070200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:178069600-178070200	Enhancers	Spleen	Spleen

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