Variant report

Variant	rs2298727
Chromosome Location	chr4:90742861-90742862
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10025915	0.80[EUR][1000 genomes]
rs10516845	0.80[EUR][1000 genomes]
rs10516847	0.98[ASN][1000 genomes]
rs11931062	0.80[EUR][1000 genomes]
rs11935469	0.80[EUR][1000 genomes]
rs11944331	0.85[EUR][1000 genomes]
rs17016188	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17016193	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17016196	0.98[ASN][1000 genomes]
rs17016235	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016274	0.86[EUR][1000 genomes]
rs2298728	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2870027	0.94[ASN][1000 genomes]
rs28781297	0.87[EUR][1000 genomes]
rs34164595	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34238791	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35540244	0.98[ASN][1000 genomes]
rs35897584	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3729594	0.98[ASN][1000 genomes]
rs3775433	0.80[EUR][1000 genomes]
rs3775435	0.98[ASN][1000 genomes]
rs3775437	0.98[ASN][1000 genomes]
rs3775438	0.98[ASN][1000 genomes]
rs3775442	0.98[ASN][1000 genomes]
rs3775444	0.98[ASN][1000 genomes]
rs3775450	1.00[ASN][1000 genomes]
rs3775453	1.00[ASN][1000 genomes]
rs3796662	0.98[ASN][1000 genomes]
rs3796667	0.94[ASN][1000 genomes]
rs3822088	0.98[ASN][1000 genomes]
rs3822091	0.97[ASN][1000 genomes]
rs3857061	0.84[EUR][1000 genomes]
rs3898322	0.98[ASN][1000 genomes]
rs3899608	0.80[EUR][1000 genomes]
rs4031753	0.87[EUR][1000 genomes]
rs58054215	0.80[EUR][1000 genomes]
rs60031383	0.80[EUR][1000 genomes]
rs6532190	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6816633	0.86[EUR][1000 genomes]
rs6826785	0.82[EUR][1000 genomes]
rs6834765	0.80[EUR][1000 genomes]
rs7655611	0.87[EUR][1000 genomes]
rs7690873	0.80[EUR][1000 genomes]
rs7698672	0.80[EUR][1000 genomes]
rs894278	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961386	1.00[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	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	chr4:90718800-90748000	Weak transcription	Brain Angular Gyrus	brain
2	chr4:90719000-90747600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr4:90722200-90751800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:90727000-90743200	Weak transcription	Fetal Lung	lung
5	chr4:90730200-90757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:90730800-90757000	Weak transcription	Fetal Stomach	stomach
7	chr4:90731600-90743000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:90734600-90743000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:90734800-90750600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:90735400-90749600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:90735800-90755600	Weak transcription	Fetal Brain Male	brain
12	chr4:90736000-90743200	Weak transcription	Ovary	ovary
13	chr4:90736200-90750600	Weak transcription	Fetal Thymus	thymus
14	chr4:90738000-90750800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:90738000-90755800	Weak transcription	Fetal Brain Female	brain
16	chr4:90738200-90750400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:90738200-90750800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr4:90738400-90745400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:90738400-90750400	Weak transcription	Brain Anterior Caudate	brain
20	chr4:90738400-90750600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:90738400-90756600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:90739400-90743800	Genic enhancers	HUVEC	blood vessel
23	chr4:90739600-90743800	Strong transcription	Dnd41	blood
24	chr4:90739600-90744400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr4:90739600-90750600	Weak transcription	Brain Hippocampus Middle	brain
26	chr4:90740000-90750600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:90740600-90750400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr4:90740800-90744200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:90741600-90743000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr4:90741600-90743000	Enhancers	NHEK	skin
31	chr4:90742000-90744800	Weak transcription	Brain Germinal Matrix	brain
32	chr4:90742000-90750600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr4:90742400-90743600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:90742400-90743600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:90742400-90744400	Weak transcription	Fetal Heart	heart
36	chr4:90742600-90743200	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr4:90742600-90744000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr4:90742600-90744400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr4:90742800-90750200	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr4:90742800-90750400	Weak transcription	HMEC	breast
41	chr4:90742800-90752200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links