Variant report

Variant	rs4658104
Chromosome Location	chr1:92087522-92087523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs58841613	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72646187	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh 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	33 gene(s)	inside rSNPs	diseases
5	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4658104	CDC7	cis	parietal	SCAN
rs4658104	F3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92075800-92088200	Weak transcription	Right Atrium	heart
2	chr1:92078000-92088200	Weak transcription	Ovary	ovary
3	chr1:92080000-92087600	Weak transcription	Fetal Heart	heart
4	chr1:92083000-92087600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:92083400-92088600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:92083400-92088600	Weak transcription	Left Ventricle	heart
7	chr1:92084000-92103200	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:92085600-92088000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:92086400-92087600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:92086600-92089200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:92086800-92087600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:92086800-92087600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:92086800-92089000	Enhancers	Colon Smooth Muscle	Colon
14	chr1:92087000-92089400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:92087200-92088600	Enhancers	Adipose Nuclei	Adipose
16	chr1:92087200-92089000	Enhancers	Aorta	Aorta
17	chr1:92087200-92089000	Enhancers	Stomach Smooth Muscle	stomach
18	chr1:92087400-92087800	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:92087400-92088400	Enhancers	NHDF-Ad	bronchial
20	chr1:92087400-92088800	Enhancers	Brain Substantia Nigra	brain
21	chr1:92087400-92088800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr1:92087400-92089000	Enhancers	Brain Anterior Caudate	brain
23	chr1:92087400-92089000	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:92087400-92089000	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:92087400-92089200	Enhancers	Brain Angular Gyrus	brain

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