Variant report

Variant	rs41343546
Chromosome Location	chr1:45908263-45908264
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12116441	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12121377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12138348	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12138495	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs3219474	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs487174	0.88[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
9	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
10	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs41343546	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs41343546	CCDC163P	cis	Artery Aorta	GTEx
rs41343546	CCDC163P	cis	lung	GTEx
rs41343546	CCDC163P	cis	Whole Blood	GTEx
rs41343546	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs41343546	CCDC163P	cis	Esophagus Muscularis	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45884600-45910600	Weak transcription	Ovary	ovary
2	chr1:45887600-45909200	Weak transcription	Liver	Liver
3	chr1:45888000-45910000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:45888200-45920600	Weak transcription	Primary B cells from cord blood	blood
5	chr1:45889800-45940600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:45902600-45924200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:45903200-45920600	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr1:45905200-45909200	Enhancers	Placenta	Placenta
9	chr1:45905200-45921000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr1:45907000-45919600	Weak transcription	Primary T cells from cord blood	blood
11	chr1:45907400-45908400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:45907400-45908600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:45907600-45908600	Enhancers	NH-A	brain
14	chr1:45907800-45908400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr1:45907800-45908400	Enhancers	HUVEC	blood vessel
16	chr1:45907800-45908400	Enhancers	NHEK	skin
17	chr1:45907800-45908400	Enhancers	Osteobl	bone
18	chr1:45908000-45908400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:45908000-45908400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr1:45908000-45908600	Enhancers	Brain Hippocampus Middle	brain
21	chr1:45908000-45909200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:45908200-45908400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:45908200-45908600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:45908200-45908600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:45908200-45908600	Enhancers	Brain Cingulate Gyrus	brain
26	chr1:45908200-45908800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:45908200-45908800	Enhancers	Fetal Intestine Large	intestine
28	chr1:45908200-45909000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr1:45908200-45911000	Enhancers	Fetal Intestine Small	intestine

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