Variant report

Variant	rs2875746
Chromosome Location	chr17:46055347-46055348
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:3)
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	CTCF	chr17:46055260-46055410	NHDF-neo	bronchial:	n/a	n/a
2	CTCF	chr17:46055200-46055350	GM12873	blood:	n/a	n/a
3	CTCF	chr17:46055200-46055350	BJ	skin:	n/a	n/a
4	CTCF	chr17:46055220-46055370	HMEC	breast:	n/a	n/a
5	CTCF	chr17:46055280-46055430	HBMEC	blood vessel:	n/a	n/a
6	CTCF	chr17:46055220-46055370	HMF	breast:	n/a	n/a
7	CTCF	chr17:46055240-46055390	HPAF	blood vessel:	n/a	n/a
8	CTCF	chr17:46055240-46055390	GM12864	blood:	n/a	n/a
9	CTCF	chr17:46055220-46055370	HFF	foreskin:	n/a	n/a
10	CTCF	chr17:46055260-46055410	AG09309	skin:	n/a	n/a
11	CTCF	chr17:46055240-46055390	GM06990	blood:	n/a	n/a
12	CTCF	chr17:46055260-46055410	GM12873	blood:	n/a	n/a
13	CTCF	chr17:46055200-46055350	AG09319	gingival:	n/a	n/a
14	CTCF	chr17:46055220-46055370	GM12873	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46047245..46051740-chr17:46053378..46057507,6	MCF-7	breast:
2	chr17:46034267..46036157-chr17:46054956..46057577,2	MCF-7	breast:
3	chr17:46024543..46026331-chr17:46053891..46056374,2	K562	blood:

No data

Variant related genes	Relation type
CDK5RAP3	TF binding region
ENSG00000264019	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11079804	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs11545723	0.94[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs1476578	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476579	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17617250	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs2003477	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003478	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2255697	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255815	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525084	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525085	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525091	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525092	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525093	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525094	0.80[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2525096	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2525098	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2525103	0.85[TSI][hapmap]
rs2597161	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597165	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2597166	0.91[AFR][1000 genomes]
rs2597168	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597171	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597172	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597173	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597174	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2597180	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2597181	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905845	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905846	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2905848	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905849	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905850	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2905853	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34190379	0.94[ASN][1000 genomes]
rs35653190	0.83[ASN][1000 genomes]
rs4793734	0.94[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs4794225	0.82[CHB][hapmap]
rs62064873	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6503949	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737130	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs739853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7406338	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7503584	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.94[ASN][1000 genomes]
rs8076314	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885634	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[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	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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2875746	PNPO	cis	cerebellum	SCAN
rs2875746	ETV4	cis	parietal	SCAN
rs2875746	ATP6V0A1	cis	parietal	SCAN
rs2875746	C17orf57	cis	parietal	SCAN
rs2875746	NFE2L1	cis	parietal	SCAN
rs2875746	PNPO	cis	parietal	SCAN
rs2875746	ASB16	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46049000-46056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:46049600-46056200	Weak transcription	Psoas Muscle	Psoas
3	chr17:46049600-46059600	Weak transcription	Fetal Heart	heart
4	chr17:46049800-46058200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:46049800-46066600	Weak transcription	Small Intestine	intestine
6	chr17:46050000-46055800	Weak transcription	Fetal Brain Male	brain
7	chr17:46050000-46056200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr17:46050200-46056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:46050200-46056000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:46050200-46060400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr17:46050200-46060400	Strong transcription	Osteobl	bone
12	chr17:46050200-46061800	Strong transcription	NHLF	lung
13	chr17:46050200-46062000	Strong transcription	NHEK	skin
14	chr17:46050200-46062200	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr17:46050200-46062800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:46050200-46063000	Strong transcription	Fetal Muscle Trunk	muscle
17	chr17:46050200-46063400	Strong transcription	Fetal Stomach	stomach
18	chr17:46050400-46056800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr17:46050400-46058000	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr17:46050400-46060800	Strong transcription	Ovary	ovary
21	chr17:46050400-46061000	Strong transcription	A549	lung
22	chr17:46050400-46061200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr17:46050400-46061400	Strong transcription	HepG2	liver
24	chr17:46050400-46062000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:46050400-46062200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:46050400-46063000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr17:46050600-46056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr17:46050600-46056000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr17:46050600-46056200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr17:46050600-46057000	Strong transcription	Dnd41	blood
31	chr17:46050600-46058000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr17:46050600-46061800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr17:46050600-46062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr17:46050600-46062200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr17:46050800-46055400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr17:46050800-46056000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr17:46050800-46056000	Strong transcription	GM12878-XiMat	blood
38	chr17:46050800-46057200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr17:46050800-46057800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr17:46050800-46058000	Strong transcription	Brain Cingulate Gyrus	brain
42	chr17:46050800-46059000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr17:46050800-46059200	Strong transcription	Liver	Liver
44	chr17:46050800-46059200	Strong transcription	Spleen	Spleen
45	chr17:46050800-46059600	Strong transcription	Brain Anterior Caudate	brain
46	chr17:46050800-46060000	Strong transcription	Brain Angular Gyrus	brain
47	chr17:46050800-46060200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr17:46050800-46060200	Strong transcription	Adipose Nuclei	Adipose
49	chr17:46050800-46060200	Strong transcription	Gastric	stomach
50	chr17:46050800-46060800	Strong transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links