Variant report

Variant	rs17563262
Chromosome Location	chr1:220240862-220240863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220239216..220241724-chr1:220243236..220244881,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11095	1.00[CEU][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap]
rs12568334	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12757995	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17563518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17563587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2053250	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2289190	0.89[CEU][hapmap]
rs3738336	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap]
rs3767654	0.88[CEU][hapmap]
rs57728897	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60531981	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61484867	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72747321	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72747325	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72747385	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72747386	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72747387	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72747389	0.81[ASN][1000 genomes]
rs72747390	0.81[ASN][1000 genomes]
rs72747391	0.81[ASN][1000 genomes]
rs7549450	0.81[ASN][1000 genomes]

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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
3	esv2753619	chr1:220210273-220302117	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	737 gene(s)	inside rSNPs	diseases
4	nsv549222	chr1:220226732-220246392	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17563262	BPNT1	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220220400-220243600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:220220400-220257600	Weak transcription	Stomach Mucosa	stomach
3	chr1:220220600-220245800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:220220600-220262400	Weak transcription	Pancreas	Pancrea
5	chr1:220220600-220262400	Weak transcription	NHLF	lung
6	chr1:220220800-220261600	Weak transcription	Fetal Brain Male	brain
7	chr1:220225800-220245800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:220227400-220245600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:220227800-220245800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:220229800-220245000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:220230000-220245800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr1:220230800-220242600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr1:220231000-220247600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:220231200-220241200	Strong transcription	Placenta	Placenta
15	chr1:220231200-220241400	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:220231200-220243200	Strong transcription	Fetal Intestine Large	intestine
17	chr1:220231200-220247800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:220231200-220248600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:220231400-220243200	Strong transcription	Adipose Nuclei	Adipose
20	chr1:220231800-220243000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr1:220232200-220241600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:220232400-220247000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:220232400-220250000	Weak transcription	Small Intestine	intestine
24	chr1:220233200-220245800	Weak transcription	Fetal Heart	heart
25	chr1:220234000-220242600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:220234400-220245800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:220234400-220247600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:220234400-220248000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:220234400-220253600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr1:220234600-220243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:220234600-220245800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:220234600-220247600	Strong transcription	Liver	Liver
33	chr1:220234800-220242800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:220234800-220242800	Strong transcription	Primary B cells from cord blood	blood
35	chr1:220234800-220243200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr1:220235000-220241400	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr1:220235000-220241400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:220235000-220241400	Strong transcription	K562	blood
39	chr1:220235000-220247400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:220235000-220247800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:220235200-220245800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:220235800-220241200	Strong transcription	Fetal Brain Female	brain
43	chr1:220235800-220242800	Strong transcription	Dnd41	blood
44	chr1:220235800-220247800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:220236000-220241200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:220236000-220241800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:220236000-220242400	Strong transcription	Primary T cells from cord blood	blood
48	chr1:220236000-220242600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr1:220236000-220242800	Strong transcription	Fetal Lung	lung
50	chr1:220236000-220242800	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links