Variant report

Variant	rs2525095
Chromosome Location	chr17:46037277-46037278
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr17:46037216-46037490	GM12878	blood:	n/a	chr17:46037390-46037401 chr17:46037391-46037400
2	EBF1	chr17:46037192-46037567	GM12878	blood:	n/a	chr17:46037390-46037401 chr17:46037391-46037400
3	POLR2A	chr17:46037113-46037283	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45925187..45928793-chr17:46033650..46037470,3	MCF-7	breast:
2	chr17:46035894..46038484-chr17:46099628..46103418,4	MCF-7	breast:
3	chr17:46033549..46039001-chr17:46046732..46050276,6	K562	blood:
4	chr17:46031321..46037809-chr17:46043555..46050276,13	K562	blood:
5	chr17:45969751..45975935-chr17:46032072..46038613,14	MCF-7	breast:
6	chr17:46009429..46012200-chr17:46035247..46037959,2	MCF-7	breast:

Variant related genes	Relation type
PRR15L	TF binding region
ENSG00000266601	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000264920	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11079802	0.87[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11651753	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs16949418	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs16949720	0.82[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2002136	0.87[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2325748	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2428608	0.93[ASN][1000 genomes]
rs2525109	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2525110	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2597169	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs2875735	0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs3764398	0.91[ASN][1000 genomes]
rs3826396	0.97[ASN][1000 genomes]
rs4793738	0.93[ASN][1000 genomes]
rs4794331	0.96[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs57768342	0.97[ASN][1000 genomes]
rs61665404	0.94[ASN][1000 genomes]
rs7207225	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs7220104	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs72823505	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2525095	MRPL10	cis	Whole Blood	GTEx
rs2525095	SKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
2	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
3	chr17:46027600-46047400	Weak transcription	Right Ventricle	heart
4	chr17:46027600-46047600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr17:46028000-46047400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr17:46028000-46047600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46030200-46045800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr17:46031400-46039000	Weak transcription	Primary T cells from cord blood	blood
9	chr17:46032000-46037800	Active TSS	Rectal Smooth Muscle	rectum
10	chr17:46032800-46037800	Enhancers	Fetal Thymus	thymus
11	chr17:46035000-46047400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:46035200-46037600	Weak transcription	K562	blood
13	chr17:46035200-46038600	Weak transcription	Small Intestine	intestine
14	chr17:46035400-46038000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
15	chr17:46035600-46038000	Enhancers	Esophagus	oesophagus
16	chr17:46035800-46037600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr17:46035800-46037600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr17:46035800-46037800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:46035800-46037800	Weak transcription	NHEK	skin
20	chr17:46036000-46047200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr17:46036200-46037600	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr17:46036200-46043400	Weak transcription	A549	lung
23	chr17:46036400-46037400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:46036400-46039200	Enhancers	Pancreas	Pancrea
25	chr17:46036600-46037800	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr17:46036600-46047800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:46036800-46037600	Weak transcription	Placenta	Placenta
28	chr17:46036800-46038400	Enhancers	HepG2	liver
29	chr17:46036800-46047400	Weak transcription	Thymus	Thymus
30	chr17:46037000-46038000	Enhancers	Colonic Mucosa	Colon
31	chr17:46037000-46038400	Weak transcription	Gastric	stomach
32	chr17:46037000-46038600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr17:46037200-46037400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
34	chr17:46037200-46037800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
35	chr17:46037200-46037800	Flanking Active TSS	Fetal Intestine Large	intestine
36	chr17:46037200-46038000	Enhancers	Placenta Amnion	Placenta Amnion
37	chr17:46037200-46038000	Flanking Active TSS	Stomach Mucosa	stomach

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