Variant report

Variant	rs40215
Chromosome Location	chr5:58841346-58841347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1395335	0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs1395336	0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs294498	0.82[ASW][hapmap]
rs296406	0.89[CHB][hapmap]
rs37579	0.88[ASW][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs6858964	0.88[ASW][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs6890180	0.83[EUR][1000 genomes]
rs697076	0.82[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs702544	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs826435	0.89[AMR][1000 genomes];1.00[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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58836600-58854400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:58836800-58857400	Weak transcription	Primary B cells from cord blood	blood
3	chr5:58837600-58841400	Enhancers	Fetal Lung	lung
4	chr5:58838200-58843600	Weak transcription	Psoas Muscle	Psoas
5	chr5:58839600-58843600	Weak transcription	Gastric	stomach
6	chr5:58840000-58842200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr5:58840000-58843400	Weak transcription	Pancreas	Pancrea
8	chr5:58840000-58851600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:58840200-58843600	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:58840200-58844600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr5:58840200-58849000	Weak transcription	Fetal Intestine Small	intestine
12	chr5:58840200-58849800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:58840200-58858800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:58840400-58842400	Weak transcription	Brain Anterior Caudate	brain
15	chr5:58840400-58842400	Weak transcription	Stomach Mucosa	stomach
16	chr5:58840400-58843600	Weak transcription	Brain Angular Gyrus	brain
17	chr5:58840400-58844200	Weak transcription	Liver	Liver
18	chr5:58840400-58850800	Weak transcription	Brain Substantia Nigra	brain
19	chr5:58840400-58853200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:58840400-58856200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:58840600-58841400	Transcr. at gene 5' and 3'	A549	lung
22	chr5:58840600-58842800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:58840600-58843400	Weak transcription	Hela-S3	cervix
24	chr5:58840600-58843600	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:58840600-58844600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:58840600-58844800	Weak transcription	Small Intestine	intestine
27	chr5:58840600-58851400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:58840800-58843400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:58840800-58843400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:58840800-58843600	Weak transcription	Fetal Brain Male	brain
31	chr5:58840800-58843600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr5:58840800-58844600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:58840800-58858600	Weak transcription	Fetal Kidney	kidney
34	chr5:58841200-58841400	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links