Variant report

Variant	rs2525087
Chromosome Location	chr17:46054264-46054265
allele	A/C
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	POLR2A	chr17:46054239-46054266	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
2	chr17:46024543..46026331-chr17:46053891..46056374,2	K562	blood:

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000264019	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11079804	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs11545723	0.94[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs1476578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476579	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17617250	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2003477	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003478	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255697	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255815	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525084	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525085	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525091	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525092	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525094	0.80[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525096	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525098	1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs2525103	0.85[TSI][hapmap]
rs2597161	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597165	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597168	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597171	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597172	0.82[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];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597180	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597181	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2875746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905845	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905846	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905848	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905849	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905850	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905853	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34190379	0.94[ASN][1000 genomes]
rs35653190	0.83[ASN][1000 genomes]
rs4793734	0.94[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs4794225	0.82[CHB][hapmap]
rs62064873	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6503949	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs739853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7406338	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7503584	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[MEX][hapmap];0.94[ASN][1000 genomes]
rs8076314	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885634	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2525087	PNPO	cis	cerebellum	SCAN
rs2525087	ASB16	cis	parietal	SCAN
rs2525087	ETV4	cis	parietal	SCAN
rs2525087	NFE2L1	cis	parietal	SCAN
rs2525087	C17orf57	cis	parietal	SCAN
rs2525087	ATP6V0A1	cis	parietal	SCAN
rs2525087	PNPO	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049000-46055200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr17:46049000-46056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:46049600-46056200	Weak transcription	Psoas Muscle	Psoas
4	chr17:46049600-46059600	Weak transcription	Fetal Heart	heart
5	chr17:46049800-46058200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
7	chr17:46050000-46054800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr17:46050000-46055800	Weak transcription	Fetal Brain Male	brain
9	chr17:46050000-46056200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:46050200-46054800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr17:46050200-46056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:46050200-46056000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:46050200-46060400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr17:46050200-46060400	Strong transcription	Osteobl	bone
15	chr17:46050200-46061800	Strong transcription	NHLF	lung
16	chr17:46050200-46062000	Strong transcription	NHEK	skin
17	chr17:46050200-46062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr17:46050200-46062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:46050200-46063000	Strong transcription	Fetal Muscle Trunk	muscle
20	chr17:46050200-46063400	Strong transcription	Fetal Stomach	stomach
21	chr17:46050400-46056800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr17:46050400-46058000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr17:46050400-46060800	Strong transcription	Ovary	ovary
24	chr17:46050400-46061000	Strong transcription	A549	lung
25	chr17:46050400-46061200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr17:46050400-46061400	Strong transcription	HepG2	liver
27	chr17:46050400-46062000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:46050400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr17:46050400-46063000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr17:46050600-46056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:46050600-46056000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr17:46050600-46056200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr17:46050600-46057000	Strong transcription	Dnd41	blood
34	chr17:46050600-46058000	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr17:46050600-46061800	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr17:46050600-46062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr17:46050600-46062200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr17:46050800-46055400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr17:46050800-46056000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr17:46050800-46056000	Strong transcription	GM12878-XiMat	blood
41	chr17:46050800-46057200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:46050800-46058000	Strong transcription	Brain Cingulate Gyrus	brain
45	chr17:46050800-46059000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr17:46050800-46059200	Strong transcription	Liver	Liver
47	chr17:46050800-46059200	Strong transcription	Spleen	Spleen
48	chr17:46050800-46059600	Strong transcription	Brain Anterior Caudate	brain
49	chr17:46050800-46060000	Strong transcription	Brain Angular Gyrus	brain
50	chr17:46050800-46060200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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