Variant report

Variant	rs2546193
Chromosome Location	chr5:95193740-95193741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr5:95193720-95195741	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr5:95193203-95198379	IMR90	lung:	n/a	n/a
3	MAX	chr5:95192757-95193763	HepG2	liver:	n/a	chr5:95193307-95193316
4	MYBL2	chr5:95192829-95194051	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:95193722-95195276	U87	brain:	n/a	n/a
6	POLR2A	chr5:95193696-95201073	MCF10A-Er-Src	breast:	n/a	n/a
7	MAZ	chr5:95192747-95195753	IMR90	lung:	n/a	chr5:95193307-95193316

No.	Distal block	Cell Line	Cell type
1	chr5:95065746..95068516-chr5:95192441..95195088,2	K562	blood:
2	chr5:95192803..95195845-chr5:95402156..95405628,4	K562	blood:
3	chr5:95193159..95197035-chr5:95199083..95201765,3	K562	blood:
4	chr5:95170114..95172338-chr5:95193145..95195226,2	MCF-7	breast:
5	chr5:95193414..95195119-chr5:95295592..95298550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250362	TF binding region
ENSG00000251314	Chromatin interaction
ENSG00000118985	Chromatin interaction
ENSG00000250240	Chromatin interaction
ENSG00000164292	Chromatin interaction
ENSG00000251000	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12109442	0.85[CHB][hapmap]
rs17085159	0.85[CHB][hapmap]
rs17085165	0.85[CHB][hapmap]
rs2546194	0.83[CHD][hapmap]
rs3822751	0.80[CHB][hapmap]
rs4869251	0.85[CHB][hapmap]
rs6556883	0.85[CHB][hapmap]
rs7734301	0.81[CHB][hapmap]

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	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1019566	chr5:95180352-95300677	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2546193	C5orf27	cis	brain	BrainEAC

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95179000-95206000	Weak transcription	Spleen	Spleen
2	chr5:95186400-95194200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:95188400-95195600	Enhancers	Fetal Heart	heart
4	chr5:95188600-95194400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:95191000-95194200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:95191000-95194200	Enhancers	Brain Hippocampus Middle	brain
7	chr5:95191000-95194200	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr5:95191000-95194200	Enhancers	Brain Substantia Nigra	brain
9	chr5:95191000-95194400	Enhancers	Brain Angular Gyrus	brain
10	chr5:95191200-95194200	Enhancers	Brain Anterior Caudate	brain
11	chr5:95191200-95194200	Enhancers	Brain Cingulate Gyrus	brain
12	chr5:95191200-95194200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr5:95191800-95194000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:95191800-95194400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr5:95191800-95195800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:95191800-95195800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:95192000-95201400	Enhancers	Placenta	Placenta
18	chr5:95192200-95193800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:95192200-95194200	Enhancers	Adipose Nuclei	Adipose
20	chr5:95192200-95194200	Weak transcription	Fetal Brain Male	brain
21	chr5:95192200-95194400	Enhancers	Esophagus	oesophagus
22	chr5:95192200-95194400	Enhancers	Pancreas	Pancrea
23	chr5:95192200-95194400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr5:95192200-95194600	Enhancers	Left Ventricle	heart
25	chr5:95192200-95194600	Enhancers	Ovary	ovary
26	chr5:95192200-95194800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:95192200-95195000	Enhancers	Lung	lung
28	chr5:95192200-95195000	Enhancers	Right Atrium	heart
29	chr5:95192200-95195800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:95192200-95199400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:95192400-95194400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr5:95192400-95195400	Weak transcription	Small Intestine	intestine
33	chr5:95192400-95199200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr5:95192600-95193800	Enhancers	Liver	Liver
35	chr5:95192800-95193800	Enhancers	Hela-S3	cervix
36	chr5:95192800-95194200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:95192800-95194200	Enhancers	Aorta	Aorta
38	chr5:95192800-95194200	Enhancers	Colonic Mucosa	Colon
39	chr5:95192800-95194200	Enhancers	Colon Smooth Muscle	Colon
40	chr5:95192800-95194200	Enhancers	HSMM	muscle
41	chr5:95192800-95194400	Enhancers	Duodenum Mucosa	Duodenum
42	chr5:95192800-95194600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:95192800-95194600	Enhancers	HUVEC	blood vessel
44	chr5:95193000-95193800	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr5:95193000-95193800	Enhancers	NH-A	brain
46	chr5:95193000-95193800	Enhancers	Osteobl	bone
47	chr5:95193000-95194000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:95193000-95194000	Enhancers	Gastric	stomach
49	chr5:95193000-95194200	Enhancers	HSMMtube	muscle
50	chr5:95193000-95194600	Enhancers	Fetal Stomach	stomach

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