Variant report

Variant	rs11545723
Chromosome Location	chr17:46035180-46035181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46033378..46035935-chr17:46129952..46132940,2	MCF-7	breast:
2	chr17:45925187..45928793-chr17:46033650..46037470,3	MCF-7	breast:
3	chr17:45917897..45920844-chr17:46033567..46035986,3	MCF-7	breast:
4	chr17:46032611..46035777-chr17:46183682..46186625,3	MCF-7	breast:
5	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
6	chr17:46033818..46036436-chr17:48943075..48944680,2	MCF-7	breast:
7	chr17:46034698..46035465-chr17:46047687..46048504,2	MCF-7	breast:
8	chr17:45898563..45901614-chr17:46033321..46036165,3	MCF-7	breast:
9	chr17:46033611..46036450-chr20:45980908..45983000,2	MCF-7	breast:
10	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
11	chr17:45969751..45975935-chr17:46032072..46038613,14	MCF-7	breast:
12	chr17:46034205..46036701-chr17:46124057..46126410,2	MCF-7	breast:
13	chr17:46034267..46036157-chr17:46054956..46057577,2	MCF-7	breast:
14	chr17:45917528..45920214-chr17:46032690..46035678,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101040	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000231119	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000006025	Chromatin interaction
ENSG00000229980	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11079804	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12452082	0.88[MEX][hapmap]
rs12602494	0.83[CHB][hapmap]
rs12948368	0.85[AMR][1000 genomes]
rs1476578	0.94[CHB][hapmap]
rs1476579	0.94[CHB][hapmap];0.81[GIH][hapmap]
rs17617250	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2074191	0.88[MEX][hapmap]
rs2525087	0.94[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs2525088	0.94[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs2525090	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2525093	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2525096	0.94[CHB][hapmap];0.81[GIH][hapmap]
rs2525098	0.94[CHB][hapmap]
rs2597165	0.82[CHB][hapmap]
rs2597171	0.89[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs2597172	0.94[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs2597173	0.94[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs2597174	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2597179	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs2875746	0.94[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs2905851	0.93[CHB][hapmap]
rs2905852	0.94[CHB][hapmap]
rs3096	0.83[CHB][hapmap];0.80[MKK][hapmap]
rs34190379	0.84[ASN][1000 genomes]
rs34428844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35132293	0.82[AMR][1000 genomes]
rs35480192	0.85[AMR][1000 genomes]
rs4793693	0.85[AMR][1000 genomes]
rs4793733	0.83[CHB][hapmap]
rs4793734	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794225	0.82[CEU][hapmap];0.88[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs62067368	0.85[AMR][1000 genomes]
rs7220419	0.88[MEX][hapmap]
rs729785	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs729786	0.94[CHB][hapmap]
rs737130	0.94[CHB][hapmap]
rs739853	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7503584	0.94[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs757061	0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11545723	ASB16	cis	parietal	SCAN
rs11545723	PNPO	cis	parietal	SCAN
rs11545723	ETV4	cis	parietal	SCAN
rs11545723	NFE2L1	cis	parietal	SCAN
rs11545723	PNPO	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
2	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
3	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
4	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46029200-46035200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
8	chr17:46030200-46045800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr17:46030400-46035200	Weak transcription	Osteobl	bone
10	chr17:46030600-46035600	Active TSS	Colonic Mucosa	Colon
11	chr17:46031200-46035200	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr17:46031400-46035600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr17:46031400-46036000	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr17:46031400-46039000	Weak transcription	Primary T cells from cord blood	blood
15	chr17:46032000-46037800	Active TSS	Rectal Smooth Muscle	rectum
16	chr17:46032200-46035400	Active TSS	Stomach Mucosa	stomach
17	chr17:46032200-46036200	Active TSS	Duodenum Mucosa	Duodenum
18	chr17:46032600-46035600	Enhancers	Liver	Liver
19	chr17:46032800-46035200	Active TSS	Gastric	stomach
20	chr17:46032800-46035200	Active TSS	Small Intestine	intestine
21	chr17:46032800-46036400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:46032800-46037800	Enhancers	Fetal Thymus	thymus
23	chr17:46033000-46035200	Active TSS	Fetal Kidney	kidney
24	chr17:46033200-46035200	Active TSS	Lung	lung
25	chr17:46033200-46035400	Active TSS	Fetal Intestine Large	intestine
26	chr17:46033200-46035400	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr17:46033600-46035400	Active TSS	Pancreas	Pancrea
28	chr17:46034000-46035200	Enhancers	Thymus	Thymus
29	chr17:46034000-46035400	Flanking Active TSS	HepG2	liver
30	chr17:46034000-46035600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
31	chr17:46034000-46035600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:46034000-46036400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr17:46034200-46035200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr17:46034200-46035400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr17:46034200-46035600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:46034200-46035600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr17:46034200-46036000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr17:46034200-46036600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr17:46034200-46036600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr17:46034200-46036800	Enhancers	Placenta Amnion	Placenta Amnion
41	chr17:46034400-46035400	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr17:46034400-46035400	Flanking Active TSS	A549	lung
43	chr17:46034400-46035800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:46034400-46035800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr17:46034400-46035800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr17:46034400-46035800	Enhancers	Placenta	Placenta
47	chr17:46034600-46035200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr17:46034600-46035200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:46034600-46035200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
50	chr17:46034600-46035200	Bivalent Enhancer	Fetal Muscle Leg	muscle

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