Variant report

Variant	rs2325948
Chromosome Location	chr17:46574491-46574492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46572626..46574764-chr17:46662731..46664611,2	MCF-7	breast:
2	chr17:46574039..46576397-chr17:46577646..46580624,4	MCF-7	breast:
3	chr17:46553956..46556675-chr17:46573169..46576403,3	MCF-7	breast:
4	chr17:46569189..46572269-chr17:46574424..46577287,4	MCF-7	breast:
5	chr17:46572156..46575042-chr17:46583182..46586038,3	MCF-7	breast:
6	chr17:46573441..46575512-chr17:46598331..46600721,2	MCF-7	breast:
7	chr17:46574112..46575706-chr17:46580959..46582706,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206805	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10514953	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10853099	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10853100	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11079824	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11079825	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079826	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11079828	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs11651168	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11652125	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11652746	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11867735	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11869101	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12450225	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12603662	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1509638	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1553754	0.85[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1812501	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1987164	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2036764	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4793564	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59961340	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60154639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60859312	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62065845	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62065847	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62066684	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7214534	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72829818	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72829824	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7501529	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8077407	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs925284	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases
3	esv1002528	chr17:46566180-46575960	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2325948	PTRF	cis	parietal	SCAN
rs2325948	HOXB3	cis	Whole Blood	GTEx
rs2325948	LOC100130581	cis	parietal	SCAN
rs2325948	C17orf46	cis	parietal	SCAN
rs2325948	HOXB2	Cis_1M	lymphoblastoid	RTeQTL
rs2325948	SP6	cis	parietal	SCAN
rs2325948	HOXB-AS1	cis	Whole Blood	GTEx
rs2325948	JUP	cis	parietal	SCAN
rs2325948	PRAC	cis	parietal	SCAN
rs2325948	HOXB2	cis	multi-tissue	Pritchard
rs2325948	HOXB2	cis	Whole Blood	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46570400-46576400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr17:46570600-46574800	Enhancers	K562	blood
3	chr17:46570800-46575000	Weak transcription	Adipose Nuclei	Adipose
4	chr17:46571000-46577800	Weak transcription	Colon Smooth Muscle	Colon
5	chr17:46571200-46575400	Weak transcription	Placenta	Placenta
6	chr17:46571800-46575800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:46572600-46575600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr17:46573200-46574600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:46573200-46577200	Weak transcription	A549	lung
10	chr17:46573400-46576400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr17:46574000-46576600	Enhancers	Fetal Stomach	stomach
12	chr17:46574200-46574600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr17:46574200-46574600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr17:46574200-46574800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr17:46574200-46574800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr17:46574200-46574800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:46574200-46575200	Enhancers	NH-A	brain
18	chr17:46574200-46575800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr17:46574200-46575800	Enhancers	NHLF	lung
20	chr17:46574200-46576200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:46574200-46576200	Enhancers	Fetal Kidney	kidney
22	chr17:46574200-46576400	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr17:46574200-46576400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr17:46574200-46576800	Enhancers	NHEK	skin
25	chr17:46574200-46577800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr17:46574200-46578400	Enhancers	Muscle Satellite Cultured Cells	--
27	chr17:46574200-46578600	Enhancers	HSMM	muscle
28	chr17:46574200-46579400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:46574400-46574800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr17:46574400-46574800	Weak transcription	HSMMtube	muscle
31	chr17:46574400-46577000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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