Variant report

Variant	rs40204
Chromosome Location	chr5:89801978-89801979
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89798219..89802006-chr5:89813801..89815608,3	K562	blood:
2	chr5:89801454..89803110-chr5:89815807..89818860,3	K562	blood:
3	chr5:89801341..89803372-chr5:89815675..89817477,2	MCF-7	breast:
4	chr5:89801527..89803796-chr5:89803997..89806887,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2115500	0.89[EUR][1000 genomes]
rs2366768	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs250376	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2562515	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2562516	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2562517	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2656953	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27658	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7726781	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882364	chr5:89748142-89808531	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv882365	chr5:89770768-89882618	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 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	chr5:89771600-89814400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:89773800-89816000	Weak transcription	HepG2	liver
3	chr5:89773800-89824400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:89774000-89814600	Weak transcription	Dnd41	blood
5	chr5:89774400-89814600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:89777000-89806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:89780400-89810800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:89780600-89822600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:89783800-89813400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:89784800-89814600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:89785400-89814600	Weak transcription	NHLF	lung
12	chr5:89790200-89809600	Weak transcription	GM12878-XiMat	blood
13	chr5:89791400-89814600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr5:89791600-89813800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:89791600-89814600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:89792200-89810400	Weak transcription	Left Ventricle	heart
17	chr5:89793800-89823400	Weak transcription	Hela-S3	cervix
18	chr5:89797600-89814600	Weak transcription	Adipose Nuclei	Adipose
19	chr5:89797600-89824200	Weak transcription	Brain Angular Gyrus	brain
20	chr5:89798000-89814600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:89799600-89805200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:89799600-89817200	Weak transcription	NHDF-Ad	bronchial
23	chr5:89799800-89802200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:89799800-89814600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:89800000-89807600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:89800000-89814400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:89800000-89814600	Weak transcription	NHEK	skin
28	chr5:89800800-89803000	Strong transcription	K562	blood
29	chr5:89800800-89808200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
30	chr5:89800800-89808600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:89800800-89811600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:89800800-89814600	Weak transcription	HMEC	breast
33	chr5:89801000-89802000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:89801000-89813600	Weak transcription	NH-A	brain
35	chr5:89801000-89814600	Weak transcription	HUVEC	blood vessel
36	chr5:89801200-89809200	Weak transcription	A549	lung
37	chr5:89801400-89803000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:89801600-89802400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:89801800-89802600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr5:89801800-89803200	Strong transcription	H1 Cell Line	embryonic stem cell

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