Variant report

Variant	rs17563518
Chromosome Location	chr1:220276304-220276305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:220261085..220263110-chr1:220275764..220277863,2	MCF-7	breast:
2	chr1:220275550..220277666-chr1:220281833..220284313,2	K562	blood:
3	chr1:220267529..220269249-chr1:220275235..220276981,2	K562	blood:
4	chr1:220274759..220277050-chr1:220282694..220284313,2	K562	blood:
5	chr1:220266360..220269449-chr1:220274847..220278218,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162813	Chromatin interaction
ENSG00000067704	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11095	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12404532	1.00[ASW][hapmap];0.84[MKK][hapmap]
rs12568334	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12757995	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17563262	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[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053250	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289190	0.89[CEU][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap]
rs3738336	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3767654	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs57728897	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60531981	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61484867	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72747321	0.83[ASN][1000 genomes]
rs72747325	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72747385	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72747386	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72747387	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72747389	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72747390	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72747391	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549450	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17563518	BPNT1	cis	cerebellum	SCAN
rs17563518	EPRS	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220268400-220277400	Weak transcription	Aorta	Aorta
2	chr1:220268400-220280400	Weak transcription	Fetal Kidney	kidney
3	chr1:220268400-220283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:220268400-220287400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:220268400-220293400	Weak transcription	Stomach Mucosa	stomach
6	chr1:220268400-220330200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:220268600-220282600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:220268600-220293800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:220268800-220277400	Weak transcription	Colonic Mucosa	Colon
10	chr1:220269200-220276800	Weak transcription	HSMMtube	muscle
11	chr1:220269200-220277400	Weak transcription	Pancreas	Pancrea
12	chr1:220269200-220277600	Weak transcription	Small Intestine	intestine
13	chr1:220269200-220277600	Weak transcription	Thymus	Thymus
14	chr1:220269200-220277800	Weak transcription	Fetal Brain Male	brain
15	chr1:220269200-220279400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:220269200-220279800	Weak transcription	Gastric	stomach
17	chr1:220269200-220280800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr1:220269200-220282400	Weak transcription	Spleen	Spleen
19	chr1:220269200-220282600	Weak transcription	Esophagus	oesophagus
20	chr1:220269200-220285400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:220269200-220291600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:220269200-220291600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:220269200-220292800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:220269200-220293600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:220269400-220277000	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:220269400-220277000	Weak transcription	Hela-S3	cervix
27	chr1:220269400-220277400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:220269400-220278600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:220269400-220278600	Weak transcription	NHLF	lung
30	chr1:220269400-220280400	Weak transcription	Fetal Heart	heart
31	chr1:220269400-220283400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:220269400-220284800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:220269400-220284800	Strong transcription	Osteobl	bone
34	chr1:220269400-220291200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:220269400-220330000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr1:220269600-220278400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:220269600-220290600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:220269600-220291200	Strong transcription	Liver	Liver
39	chr1:220269600-220291400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:220269600-220291400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr1:220269600-220291400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:220269600-220291600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:220269600-220291800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:220269800-220281400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:220269800-220284800	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr1:220269800-220284800	Strong transcription	Fetal Intestine Large	intestine
47	chr1:220269800-220286400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:220269800-220286600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:220269800-220291000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:220269800-220291200	Strong transcription	Fetal Thymus	thymus

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