Variant report

Variant	rs4395040
Chromosome Location	chr15:78282533-78282534
allele	A/G
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	POLR2A	chr15:78282305-78284434	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:78282316-78283946	SK-N-MC	brain:	n/a	n/a
3	PAX5	chr15:78282486-78283317	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:78281867-78282946	PANC-1	pancreas:	n/a	n/a
5	TCF3	chr15:78282490-78283524	GM12878	blood:	n/a	n/a
6	EBF1	chr15:78282512-78282883	GM12878	blood:	n/a	chr15:78282755-78282766
7	POLR2A	chr15:78282439-78283835	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78258415..78260755-chr15:78280770..78282867,2	MCF-7	breast:
2	chr15:78275999..78279475-chr15:78281569..78284408,3	MCF-7	breast:
3	chr15:78275921..78279838-chr15:78281220..78285014,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259792	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1004855	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs10519181	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11072716	0.95[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs11072717	0.85[ASN][1000 genomes]
rs11630564	0.83[ASN][1000 genomes]
rs11631578	0.95[CHB][hapmap]
rs11634607	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs12148365	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs12372950	0.87[ASN][1000 genomes]
rs12439578	0.85[ASN][1000 genomes]
rs12591354	0.95[ASN][1000 genomes]
rs12591418	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs12592891	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12593545	1.00[ASW][hapmap];0.86[MEX][hapmap]
rs12594823	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs12901812	0.91[CHB][hapmap];0.93[CHD][hapmap]
rs12911332	1.00[CHB][hapmap]
rs12916362	0.91[CHB][hapmap]
rs1348257	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1442293	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs1837913	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs1992470	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2028546	0.86[CHB][hapmap]
rs2044099	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs2241885	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs28391804	0.90[ASN][1000 genomes]
rs28560025	0.88[ASN][1000 genomes]
rs2867985	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap]
rs34940027	0.90[ASN][1000 genomes]
rs3784326	1.00[ASW][hapmap]
rs3803380	0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.88[MKK][hapmap]
rs4886553	0.95[CHB][hapmap]
rs4886554	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs4886555	0.84[AMR][1000 genomes]
rs4886992	1.00[ASW][hapmap];0.86[MEX][hapmap]
rs4886996	0.95[CHB][hapmap]
rs4886999	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs4887000	0.91[CHB][hapmap]
rs55704745	0.87[AMR][1000 genomes]
rs56317829	0.84[AMR][1000 genomes]
rs57220134	0.82[AMR][1000 genomes]
rs60497311	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62008651	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7170746	0.95[CHB][hapmap]
rs7173128	1.00[CHB][hapmap];0.93[CHD][hapmap]
rs7173473	0.87[ASN][1000 genomes]
rs7174489	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs72732535	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7495018	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030713	0.85[AMR][1000 genomes]
rs8030873	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs894301	1.00[ASW][hapmap]

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	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4395040	IREB2	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78276000-78285200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:78276600-78282800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:78277600-78285600	Enhancers	Placenta	Placenta
4	chr15:78278400-78288800	Enhancers	Fetal Muscle Leg	muscle
5	chr15:78279400-78282600	Enhancers	Esophagus	oesophagus
6	chr15:78279400-78287600	Enhancers	Fetal Heart	heart
7	chr15:78279400-78287800	Enhancers	Adipose Nuclei	Adipose
8	chr15:78279400-78289800	Enhancers	Ovary	ovary
9	chr15:78279600-78283200	Weak transcription	Brain Germinal Matrix	brain
10	chr15:78279800-78282600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:78279800-78282800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:78279800-78283400	Enhancers	Stomach Smooth Muscle	stomach
13	chr15:78279800-78289600	Weak transcription	Fetal Brain Female	brain
14	chr15:78280000-78282600	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:78280000-78282800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:78280000-78282800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:78280000-78282800	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:78280000-78282800	Weak transcription	A549	lung
19	chr15:78280000-78283000	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr15:78280000-78284400	Enhancers	Spleen	Spleen
21	chr15:78280000-78285400	Enhancers	Fetal Thymus	thymus
22	chr15:78280000-78290400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:78280200-78282600	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:78280200-78283000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:78280200-78283000	Weak transcription	Brain Cingulate Gyrus	brain
26	chr15:78280200-78284000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:78280200-78295800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:78280400-78282600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:78280400-78282800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:78280400-78282800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:78280600-78284600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr15:78280800-78282600	Weak transcription	Brain Substantia Nigra	brain
33	chr15:78280800-78282600	Weak transcription	Stomach Mucosa	stomach
34	chr15:78280800-78283200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr15:78280800-78283400	Enhancers	Thymus	Thymus
36	chr15:78280800-78285800	Enhancers	Lung	lung
37	chr15:78280800-78286400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:78280800-78287600	Enhancers	Right Ventricle	heart
39	chr15:78281000-78282600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:78281000-78282600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:78281000-78282600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:78281000-78282600	Weak transcription	Brain Angular Gyrus	brain
43	chr15:78281000-78282600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr15:78281000-78285000	Enhancers	Fetal Lung	lung
45	chr15:78281000-78289600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:78281200-78283800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:78281200-78284600	Enhancers	HSMM	muscle
48	chr15:78281200-78285400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr15:78281200-78287000	Enhancers	Pancreas	Pancrea
50	chr15:78281400-78284600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links