Variant report

Variant	rs2035268
Chromosome Location	chr4:90756077-90756078
allele	G/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	E2F4	chr4:90755968-90756163	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000247775	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10002435	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10014396	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10018362	0.83[ASN][1000 genomes]
rs10433953	0.92[AFR][1000 genomes]
rs1442137	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[LWK][hapmap]
rs17016168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17016183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17016190	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17016255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34410265	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34506386	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs34634504	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34699553	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3756055	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3756056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756057	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3775427	0.81[YRI][hapmap]
rs3775443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3775448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3775458	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3775461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3796661	1.00[ASW][hapmap];0.83[YRI][hapmap]
rs3889916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3889917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3906824	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56270968	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59398886	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60642683	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61027512	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6829514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7665887	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7684637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7684892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7689942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][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	esv2830400	chr4:90085456-90922432	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012406	chr4:90167781-91166787	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv949454	chr4:90272120-91156917	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv879536	chr4:90678541-90775212	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90730200-90757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:90730800-90757000	Weak transcription	Fetal Stomach	stomach
3	chr4:90738400-90756600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr4:90743400-90756600	Weak transcription	NHEK	skin
5	chr4:90743400-90757400	Weak transcription	Gastric	stomach
6	chr4:90743800-90756600	Weak transcription	Ovary	ovary
7	chr4:90751000-90756600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:90751000-90756600	Weak transcription	Fetal Thymus	thymus
9	chr4:90751000-90757200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:90751200-90756400	Weak transcription	Primary T cells from cord blood	blood
11	chr4:90751200-90756600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:90751400-90756600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:90751400-90756600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr4:90751400-90757400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:90751600-90756600	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:90751600-90756800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr4:90752000-90757000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr4:90752600-90756600	Weak transcription	Fetal Lung	lung
19	chr4:90753400-90756600	Genic enhancers	Dnd41	blood
20	chr4:90753600-90756600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr4:90753800-90757200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:90754600-90756400	Weak transcription	HMEC	breast
23	chr4:90755400-90756400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:90755600-90756200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:90755600-90756200	Enhancers	Fetal Brain Male	brain
26	chr4:90755600-90756400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:90755600-90756600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
28	chr4:90755600-90757000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr4:90755600-90757000	Enhancers	Brain Angular Gyrus	brain
30	chr4:90755600-90759800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:90755800-90756400	Enhancers	Brain Substantia Nigra	brain
32	chr4:90755800-90759600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:90755800-90759600	Active TSS	Fetal Brain Female	brain
34	chr4:90756000-90756200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:90756000-90756600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:90756000-90756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:90756000-90756600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:90756000-90756600	Weak transcription	Brain Anterior Caudate	brain
39	chr4:90756000-90756600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr4:90756000-90756800	Enhancers	Brain Cingulate Gyrus	brain
41	chr4:90756000-90757000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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