Variant report

Variant	rs2994669
Chromosome Location	chr1:45886349-45886350
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	chr1:45885095..45887233-chr1:45985675..45987576,2	K562	blood:
2	chr1:45885122..45886764-chr1:45955576..45958064,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070759	Chromatin interaction
ENSG00000117450	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12022634	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2994669	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs2994669	CCDC163P	cis	Muscle Skeletal	GTEx
rs2994669	CCDC163P	cis	Artery Tibial	GTEx
rs2994669	CCDC163P	cis	Whole Blood	GTEx
rs2994669	CCDC163P	cis	lung	GTEx
rs2994669	CCDC163P	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45841400-45889200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:45875600-45889400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:45876800-45887800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:45877000-45886800	Weak transcription	Liver	Liver
5	chr1:45877200-45887800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:45877200-45888200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:45877400-45886800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:45877400-45889200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:45877600-45887400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:45877600-45889600	Weak transcription	Placenta	Placenta
11	chr1:45879000-45887200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:45879600-45887800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr1:45879600-45887800	Weak transcription	Brain Anterior Caudate	brain
14	chr1:45879800-45889200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:45880000-45887000	Weak transcription	Primary B cells from cord blood	blood
16	chr1:45880200-45895600	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:45880800-45890000	Weak transcription	Brain Substantia Nigra	brain
18	chr1:45881400-45886800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:45882600-45886600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr1:45882600-45886800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:45883000-45888000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:45884200-45888800	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:45884600-45910600	Weak transcription	Ovary	ovary
24	chr1:45885400-45886800	Strong transcription	Fetal Intestine Small	intestine
25	chr1:45885400-45887000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:45885400-45890200	Weak transcription	Left Ventricle	heart
27	chr1:45885800-45886800	Weak transcription	Fetal Stomach	stomach
28	chr1:45885800-45887600	Weak transcription	Fetal Lung	lung
29	chr1:45886000-45889800	Weak transcription	Gastric	stomach

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