Variant report

Variant	rs17563877
Chromosome Location	chr5:74998892-74998893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:74998769..75000533-chr5:75008112..75009856,2	MCF-7	breast:
2	chr5:74997231..74999217-chr5:75000460..75002166,2	K562	blood:
3	chr5:74996831..74999207-chr5:75004311..75007242,2	K562	blood:

Variant related genes	Relation type
ENSG00000207333	Chromatin interaction
ENSG00000152359	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10515213	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563589	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17563700	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563974	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17563995	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17649055	0.87[CHD][hapmap]
rs17649248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17649350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17649362	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291630	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2307112	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2307113	0.87[CHD][hapmap]
rs2307115	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253387	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs253390	0.82[CHD][hapmap]
rs34355	0.94[GIH][hapmap];0.85[MEX][hapmap]
rs34356	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs34357	0.83[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap]
rs34905687	0.87[CHD][hapmap]
rs3797581	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4703676	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704231	0.87[CHD][hapmap]
rs4704233	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58255973	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58968428	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72633981	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72633982	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633983	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72633984	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72633985	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72633986	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72633987	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72633988	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72633989	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72633990	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7380748	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs888788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv830353	chr5:74961520-75152609	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17563877	POC5	cis	Thyroid	GTEx
rs17563877	TNPO1	cis	cerebellum	SCAN
rs17563877	POC5	cis	cerebellum	SCAN
rs17563877	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74965200-75011800	Weak transcription	Brain Germinal Matrix	brain
2	chr5:74965400-75012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:74965400-75012400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr5:74965400-75012400	Weak transcription	Right Ventricle	heart
5	chr5:74965600-75010400	Weak transcription	Gastric	stomach
6	chr5:74965600-75011400	Weak transcription	Small Intestine	intestine
7	chr5:74971200-75012400	Weak transcription	Aorta	Aorta
8	chr5:74971200-75012400	Weak transcription	Brain Substantia Nigra	brain
9	chr5:74979000-75003800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:74980000-75012200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:74981400-74999200	Weak transcription	Fetal Stomach	stomach
12	chr5:74981400-74999600	Weak transcription	Fetal Intestine Small	intestine
13	chr5:74981400-75002600	Weak transcription	Pancreas	Pancrea
14	chr5:74984200-75012400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr5:74986800-75000000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:74986800-75005800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:74987800-75002600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr5:74990000-75012000	Weak transcription	HSMMtube	muscle
19	chr5:74990000-75012400	Weak transcription	Esophagus	oesophagus
20	chr5:74992000-75012400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr5:74992400-75005800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:74992600-75012600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:74996400-75006400	Weak transcription	Stomach Mucosa	stomach
24	chr5:74996800-75012400	Weak transcription	Fetal Brain Male	brain
25	chr5:74997600-74999000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr5:74997600-74999000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:74997600-74999000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:74997600-74999000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:74997600-74999000	Strong transcription	Adipose Nuclei	Adipose
30	chr5:74997600-74999000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:74997600-74999000	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr5:74997600-74999000	Strong transcription	Rectal Smooth Muscle	rectum
33	chr5:74997600-74999000	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr5:74997600-74999000	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:74997600-74999000	Strong transcription	NHEK	skin
36	chr5:74997600-74999200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:74997600-74999200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr5:74997600-74999200	Strong transcription	Fetal Lung	lung
39	chr5:74997600-74999200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr5:74997600-74999400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:74997600-74999600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:74997600-75000600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr5:74997600-75000600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:74997600-75000600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:74997600-75000800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:74997600-75000800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr5:74997600-75000800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:74997600-75001000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr5:74997600-75001000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:74997600-75001000	Strong transcription	Fetal Thymus	thymus

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