Variant report

Variant	rs4794225
Chromosome Location	chr17:45957591-45957592
allele	G/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:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45954517..45959288-chr17:45971279..45974982,5	MCF-7	breast:
2	chr17:45957419..45959674-chr17:45964404..45967485,3	K562	blood:
3	chr17:45955663..45958108-chr17:45961130..45962855,2	K562	blood:
4	chr17:45927022..45929446-chr17:45953894..45957951,3	K562	blood:
5	chr17:45955819..45958170-chr17:45960377..45962855,3	K562	blood:
6	chr17:45908333..45910422-chr17:45956313..45959153,2	K562	blood:
7	chr17:45949402..45954335-chr17:45955513..45959303,4	K562	blood:
8	chr17:45954484..45959209-chr17:45960047..45963266,6	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP6-1	chr17:45956838-45959764	ENSG00000266821.1

No data

Variant related genes	Relation type
ENSG00000167182	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000264920	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11079804	0.82[CEU][hapmap];0.94[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11545723	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]
rs11654010	0.89[CHB][hapmap]
rs12452082	0.84[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.81[AMR][1000 genomes]
rs12948368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476578	0.82[CHB][hapmap]
rs1476579	0.82[CHB][hapmap]
rs17617250	0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2074191	0.94[MEX][hapmap]
rs2525087	0.82[CHB][hapmap]
rs2525088	0.82[CHB][hapmap]
rs2525090	0.82[CHB][hapmap]
rs2525093	0.88[CHB][hapmap]
rs2525096	0.82[CHB][hapmap]
rs2525098	0.82[CHB][hapmap]
rs2597172	0.82[CHB][hapmap]
rs2597173	0.82[CHB][hapmap]
rs2597174	0.82[CHB][hapmap]
rs2597179	0.82[CHB][hapmap]
rs2875746	0.82[CHB][hapmap]
rs2905852	0.82[CHB][hapmap]
rs34428844	0.85[AMR][1000 genomes]
rs35004787	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35132293	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35480192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35533494	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35702577	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4793693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4793734	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]
rs56119022	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62067368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66721410	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7220419	0.94[MEX][hapmap]
rs729785	0.82[CHB][hapmap]
rs729786	0.82[CHB][hapmap]
rs737130	0.81[CHB][hapmap]
rs739853	0.82[CHB][hapmap]
rs7503584	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs757061	0.94[MEX][hapmap]

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	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	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
rs4794225	ETV4	cis	parietal	SCAN
rs4794225	NFE2L1	cis	parietal	SCAN
rs4794225	PNPO	cis	parietal	SCAN
rs4794225	DCAKD	cis	cerebellum	SCAN
rs4794225	PNPO	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45954600-45964400	Enhancers	Fetal Intestine Large	intestine
2	chr17:45955800-45959400	Weak transcription	Fetal Kidney	kidney
3	chr17:45956200-45957800	Enhancers	Fetal Thymus	thymus
4	chr17:45956200-45959000	Weak transcription	Lung	lung
5	chr17:45956400-45959200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr17:45956400-45959600	Weak transcription	Fetal Lung	lung
7	chr17:45956400-45961600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr17:45956400-45961800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:45956400-45962400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr17:45956600-45957600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr17:45956600-45957600	Weak transcription	Fetal Intestine Small	intestine
12	chr17:45956600-45958200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr17:45956600-45959000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:45956600-45959600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr17:45956600-45961200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr17:45956600-45961800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr17:45956600-45961800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr17:45956600-45962000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr17:45956800-45959200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr17:45956800-45959200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr17:45956800-45959200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr17:45956800-45959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:45956800-45959200	Weak transcription	NHDF-Ad	bronchial
24	chr17:45956800-45959400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr17:45956800-45959400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr17:45956800-45959600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:45956800-45959600	Weak transcription	HMEC	breast
28	chr17:45956800-45959600	Weak transcription	HSMMtube	muscle
29	chr17:45956800-45960400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr17:45956800-45961800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr17:45957000-45958400	Weak transcription	K562	blood
32	chr17:45957000-45959000	Weak transcription	Osteobl	bone
33	chr17:45957000-45959200	Weak transcription	HSMM	muscle
34	chr17:45957000-45959400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr17:45957200-45958200	Weak transcription	Placenta	Placenta

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