Variant report

Variant	rs10520717
Chromosome Location	chr15:93516911-93516912
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93441189..93443550-chr15:93516285..93518087,2	MCF-7	breast:
2	chr15:93511174..93514102-chr15:93516805..93519386,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10520719	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1074513	0.87[JPT][hapmap]
rs11074127	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11630052	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11630582	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631553	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11632522	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11634204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11634207	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11634566	0.81[JPT][hapmap]
rs11637047	0.83[AMR][1000 genomes]
rs11637185	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11857145	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12438635	0.81[JPT][hapmap]
rs12594991	0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs12901950	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12904680	0.86[CEU][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12906132	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907579	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12909677	0.87[JPT][hapmap]
rs12915072	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12916015	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1534779	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17525800	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2033844	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2119010	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2272457	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2272459	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28540863	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28668136	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34026217	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34234400	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34266454	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34498571	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs35327372	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35477598	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35596808	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36048863	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3784786	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817597	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs3826035	0.87[JPT][hapmap]
rs4778062	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4778065	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4778067	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56358327	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66726419	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67190144	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs72761955	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
3	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
4	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
7	esv3422587	chr15:93514773-93517321	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3328068	chr15:93515098-93517096	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10520717	CSF2RB	trans	lymphoblastoid	seeQTL
rs10520717	ZNF710	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93493200-93533000	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr15:93493200-93536000	Strong transcription	HSMM	muscle
3	chr15:93493200-93571000	Strong transcription	Dnd41	blood
4	chr15:93493200-93571200	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr15:93493400-93548000	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr15:93493400-93568600	Strong transcription	Liver	Liver
7	chr15:93493400-93569600	Strong transcription	Placenta	Placenta
8	chr15:93493400-93571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:93493400-93571000	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr15:93493600-93521600	Strong transcription	Osteobl	bone
11	chr15:93493600-93523400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:93493600-93571400	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:93493800-93522400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr15:93493800-93532600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:93493800-93561400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr15:93493800-93571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:93494000-93520800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:93494000-93568200	Strong transcription	Fetal Thymus	thymus
19	chr15:93494000-93570400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:93494000-93570800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:93494000-93571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:93494000-93571400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:93494400-93540600	Strong transcription	Primary T cells from cord blood	blood
24	chr15:93495000-93524800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:93496600-93525800	Weak transcription	Stomach Mucosa	stomach
26	chr15:93497600-93517800	Weak transcription	Esophagus	oesophagus
27	chr15:93501400-93524000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr15:93501600-93521600	Strong transcription	NH-A	brain
29	chr15:93502400-93523600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr15:93504000-93523400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:93504000-93567800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:93505000-93569800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:93506000-93569800	Strong transcription	HepG2	liver
34	chr15:93506400-93561800	Strong transcription	A549	lung
35	chr15:93506400-93569600	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:93507000-93532800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:93507400-93517800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr15:93507800-93517800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr15:93508000-93532600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:93509600-93519800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr15:93509600-93520000	Strong transcription	Fetal Brain Female	brain
42	chr15:93509600-93522200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr15:93509600-93522400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:93509600-93525000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:93509600-93535400	Strong transcription	Fetal Muscle Leg	muscle
46	chr15:93509600-93542400	Strong transcription	Hela-S3	cervix
47	chr15:93509600-93568000	Strong transcription	Primary B cells from cord blood	blood
48	chr15:93509600-93569600	Strong transcription	NHDF-Ad	bronchial
49	chr15:93509600-93571200	Strong transcription	Fetal Lung	lung
50	chr15:93509600-93571400	Strong transcription	Duodenum Mucosa	Duodenum

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