Variant report

Variant	rs9309054
Chromosome Location	chr2:40598041-40598042
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40586222..40589135-chr2:40597627..40599804,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10182686	0.80[EUR][1000 genomes]
rs10187203	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12474472	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13405465	0.81[EUR][1000 genomes]
rs2216009	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4395287	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4952410	0.92[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4952614	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6712494	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6712622	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732915	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6742210	0.93[JPT][hapmap]
rs7581508	0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs7581611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs918001	0.92[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs994249	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873915	chr2:40573350-40615520	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40591000-40598400	Weak transcription	Fetal Stomach	stomach
2	chr2:40591600-40600800	Weak transcription	Psoas Muscle	Psoas
3	chr2:40592200-40598400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:40592200-40598800	Weak transcription	Left Ventricle	heart
5	chr2:40592400-40598400	Weak transcription	Brain Anterior Caudate	brain
6	chr2:40592400-40598400	Weak transcription	Fetal Kidney	kidney
7	chr2:40592400-40598600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:40592400-40598800	Weak transcription	Ovary	ovary
9	chr2:40592400-40605200	Weak transcription	Right Atrium	heart
10	chr2:40592800-40606600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:40593400-40607000	Weak transcription	Dnd41	blood
12	chr2:40594200-40605200	Weak transcription	Fetal Brain Female	brain
13	chr2:40595000-40598400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:40595000-40598800	Weak transcription	Fetal Brain Male	brain
15	chr2:40595000-40611000	Weak transcription	Right Ventricle	heart
16	chr2:40595200-40598400	Weak transcription	Hela-S3	cervix
17	chr2:40596000-40601600	Enhancers	Colon Smooth Muscle	Colon
18	chr2:40596400-40598400	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:40596400-40598800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:40596400-40600400	Enhancers	HSMM	muscle
21	chr2:40596400-40601200	Enhancers	Rectal Smooth Muscle	rectum
22	chr2:40596400-40601400	Enhancers	Osteobl	bone
23	chr2:40596600-40598600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:40596600-40599800	Enhancers	NH-A	brain
25	chr2:40597000-40601200	Enhancers	HSMMtube	muscle
26	chr2:40597000-40603400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr2:40597200-40598600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:40597200-40599000	Enhancers	NHDF-Ad	bronchial
29	chr2:40597200-40601400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:40597400-40598200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:40597400-40598400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:40597400-40600200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:40597400-40600600	Enhancers	Stomach Smooth Muscle	stomach
34	chr2:40597400-40600800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:40597600-40598800	Weak transcription	HMEC	breast
36	chr2:40598000-40598200	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr2:40598000-40598200	Flanking Active TSS	Fetal Heart	heart
38	chr2:40598000-40599000	Enhancers	NHLF	lung
39	chr2:40598000-40600600	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr2:40598000-40601000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links