Variant report

Variant	rs4378657
Chromosome Location	chr17:46023694-46023695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr17:46023532-46023918	HL-60	blood:	n/a	n/a
2	CTCF	chr17:46023600-46023750	BJ	skin:	n/a	n/a
3	HEY1	chr17:46023315-46023791	HepG2	liver:	n/a	n/a
4	SPI1	chr17:46023567-46023838	K562	blood:	n/a	n/a
5	MAZ	chr17:46023622-46023779	HepG2	liver:	n/a	n/a
6	SPI1	chr17:46023421-46023990	HL-60	blood:	n/a	n/a
7	SPI1	chr17:46023581-46023824	K562	blood:	n/a	n/a
8	SPI1	chr17:46023594-46023778	GM12878	blood:	n/a	n/a
9	SPI1	chr17:46023463-46023897	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:46023608-46024788	MCF10A-Er-Src	breast:	n/a	n/a
11	SPI1	chr17:46023337-46024001	GM12878	blood:	n/a	n/a
12	SPI1	chr17:46023579-46023901	GM12891	blood:	n/a	n/a
13	CTCF	chr17:46023599-46024886	A549	lung:	n/a	n/a
14	SPI1	chr17:46023552-46023898	GM12891	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45995492..45998307-chr17:46023078..46025129,2	MCF-7	breast:
2	chr17:45970281..45975378-chr17:46022719..46027732,11	MCF-7	breast:
3	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
4	chr17:46008254..46011151-chr17:46023044..46026189,3	MCF-7	breast:
5	chr17:45918596..45919178-chr17:46023683..46024868,3	MCF-7	breast:
6	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
7	chr17:45913355..45915258-chr17:46023188..46024745,2	MCF-7	breast:
8	chr17:46021116..46023804-chr17:46125669..46127456,2	K562	blood:
9	chr17:45920330..45920951-chr17:46023036..46023982,2	MCF-7	breast:
10	chr17:45976149..45977762-chr17:46023014..46025634,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000234494	TF binding region
ENSG00000266601	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10491182	0.87[GIH][hapmap]
rs10491183	0.87[GIH][hapmap]
rs11650043	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11650304	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11651625	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16949676	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17617360	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17618704	0.81[GIH][hapmap];1.00[MEX][hapmap]
rs17679445	0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41429650	0.87[GIH][hapmap]
rs7209072	0.87[GIH][hapmap]
rs9895554	0.82[GIH][hapmap]
rs9903963	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4378657	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019600-46027000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46019800-46024000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr17:46019800-46024800	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr17:46019800-46025600	Weak transcription	HSMM	muscle
5	chr17:46019800-46026800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr17:46019800-46026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr17:46019800-46026800	Weak transcription	Brain Germinal Matrix	brain
8	chr17:46019800-46026800	Weak transcription	HSMMtube	muscle
9	chr17:46019800-46027400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
12	chr17:46020000-46024000	Weak transcription	Colon Smooth Muscle	Colon
13	chr17:46020000-46024400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr17:46020000-46026000	Weak transcription	Fetal Heart	heart
15	chr17:46020000-46026200	Weak transcription	Fetal Kidney	kidney
16	chr17:46020000-46026400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr17:46020000-46026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr17:46020000-46026400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr17:46020000-46026800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:46020000-46026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr17:46020000-46027000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr17:46020200-46026000	Weak transcription	NHDF-Ad	bronchial
24	chr17:46020200-46026200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr17:46020200-46026200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr17:46020200-46026800	Weak transcription	HUVEC	blood vessel
27	chr17:46020600-46024800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr17:46020800-46024200	Strong transcription	NHEK	skin
29	chr17:46020800-46024400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr17:46020800-46024800	Genic enhancers	Osteobl	bone
31	chr17:46020800-46025800	Genic enhancers	HepG2	liver
32	chr17:46021000-46024200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr17:46021000-46024200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:46021000-46024800	Strong transcription	Dnd41	blood
35	chr17:46021000-46024800	Genic enhancers	GM12878-XiMat	blood
36	chr17:46021200-46023800	Enhancers	Stomach Mucosa	stomach
37	chr17:46021200-46024000	Strong transcription	Lung	lung
38	chr17:46021200-46024200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr17:46021200-46024200	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr17:46021400-46024000	Strong transcription	K562	blood
41	chr17:46021400-46024200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr17:46021600-46024200	Strong transcription	Fetal Stomach	stomach
43	chr17:46021600-46024600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr17:46021600-46026200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr17:46021800-46024200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:46021800-46024200	Genic enhancers	Rectal Mucosa Donor 29	rectum
47	chr17:46021800-46024200	Strong transcription	Spleen	Spleen
48	chr17:46021800-46024400	Genic enhancers	Pancreas	Pancrea
49	chr17:46021800-46024400	Genic enhancers	Thymus	Thymus
50	chr17:46021800-46024800	Genic enhancers	Primary T cells fromperipheralblood	blood

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