Variant report

Variant	rs4907140
Chromosome Location	chr1:85663699-85663700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85641812..85644016-chr1:85661347..85664205,2	K562	blood:
2	chr1:85653773..85655948-chr1:85662257..85664650,2	MCF-7	breast:
3	chr1:85658898..85664597-chr1:85664894..85668250,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000097096	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11161543	0.90[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12026642	0.90[CEU][hapmap];0.84[JPT][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs55806921	0.81[ASN][1000 genomes]
rs61136219	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6668323	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv1792086	chr1:85644478-85667608	Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv546701	chr1:85662851-85667386	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv546702	chr1:85663699-85667356	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv1800754	chr1:85663699-85667557	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv1801195	chr1:85663699-85667608	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv1811802	chr1:85663699-85667608	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	esv1812785	chr1:85663699-85667608	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4907140	C1orf52	cis	cerebellum	SCAN
rs4907140	LOC339524	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85615800-85665800	Weak transcription	Esophagus	oesophagus
2	chr1:85627800-85664400	Weak transcription	Osteobl	bone
3	chr1:85639000-85665400	Weak transcription	Placenta	Placenta
4	chr1:85644200-85664400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:85645800-85663800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:85646000-85664800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr1:85646600-85665200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:85646800-85663800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:85647200-85664400	Weak transcription	Fetal Kidney	kidney
10	chr1:85648400-85665200	Weak transcription	Ovary	ovary
11	chr1:85648400-85665200	Weak transcription	HSMM	muscle
12	chr1:85648800-85664600	Weak transcription	NH-A	brain
13	chr1:85649200-85665800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:85653600-85664200	Weak transcription	HMEC	breast
15	chr1:85654000-85664800	Weak transcription	HUVEC	blood vessel
16	chr1:85654000-85665600	Weak transcription	Brain Anterior Caudate	brain
17	chr1:85654400-85665600	Weak transcription	Brain Substantia Nigra	brain
18	chr1:85654400-85665800	Weak transcription	Gastric	stomach
19	chr1:85654400-85665800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:85654800-85664600	Weak transcription	Colonic Mucosa	Colon
21	chr1:85654800-85665600	Weak transcription	Pancreas	Pancrea
22	chr1:85656000-85664000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:85656000-85664600	Weak transcription	Fetal Stomach	stomach
24	chr1:85656000-85664600	Weak transcription	NHLF	lung
25	chr1:85656000-85665600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:85656200-85663800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:85656200-85663800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:85656200-85663800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr1:85656200-85664200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:85656200-85664600	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:85656200-85664600	Weak transcription	Fetal Intestine Small	intestine
32	chr1:85656200-85665800	Weak transcription	Lung	lung
33	chr1:85656400-85663800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:85656400-85663800	Weak transcription	Fetal Lung	lung
35	chr1:85656400-85664600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:85656400-85665200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:85656400-85665400	Weak transcription	HSMMtube	muscle
38	chr1:85656400-85665600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:85659600-85663800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:85661000-85669000	Active TSS	Stomach Smooth Muscle	stomach
41	chr1:85661200-85664400	Enhancers	Liver	Liver
42	chr1:85661400-85668400	Active TSS	Colon Smooth Muscle	Colon
43	chr1:85661600-85663800	Weak transcription	Aorta	Aorta
44	chr1:85661600-85665200	Weak transcription	GM12878-XiMat	blood
45	chr1:85661800-85663800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:85661800-85663800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:85661800-85663800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:85661800-85665600	Weak transcription	Brain Angular Gyrus	brain
49	chr1:85661800-85665800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:85662000-85663800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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