Variant report

Variant	rs40126
Chromosome Location	chr5:58650933-58650934
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs154031	0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs168641	0.87[ASN][1000 genomes]
rs2441091	0.82[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs244573	0.86[AFR][1000 genomes]
rs244574	0.93[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs244575	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs244577	0.95[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs244579	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs244582	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs244583	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs244586	0.83[ASN][1000 genomes]
rs244588	0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs244591	0.87[YRI][hapmap]
rs35258	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs35263	0.89[EUR][1000 genomes]
rs35267	0.95[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35274	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35276	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35278	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35279	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35283	0.86[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs35284	0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs39672	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs40328	0.92[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs434274	0.82[YRI][hapmap]

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	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1032732	chr5:58637179-58689010	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1022160	chr5:58645805-58689010	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	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	chr5:58635200-58652600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:58642200-58653200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:58642600-58652600	Weak transcription	Fetal Brain Male	brain
4	chr5:58642600-58652600	Weak transcription	Small Intestine	intestine
5	chr5:58643600-58652400	Weak transcription	Fetal Kidney	kidney
6	chr5:58646200-58654400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:58648000-58652600	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:58648000-58654200	Weak transcription	Ovary	ovary
9	chr5:58648200-58652200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr5:58648200-58652200	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr5:58648400-58652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:58648400-58652600	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:58648600-58652200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr5:58648600-58652600	Weak transcription	Brain Angular Gyrus	brain
15	chr5:58648600-58652600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:58648600-58653000	Active TSS	Right Ventricle	heart
17	chr5:58648600-58653400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:58648600-58653800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:58649000-58652600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:58649000-58652600	Weak transcription	Fetal Stomach	stomach
21	chr5:58649400-58652600	Active TSS	Right Atrium	heart
22	chr5:58649400-58652800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:58649400-58653600	Weak transcription	Brain Anterior Caudate	brain
24	chr5:58649400-58653600	Weak transcription	Brain Substantia Nigra	brain
25	chr5:58649400-58654000	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr5:58649400-58654200	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr5:58649600-58651400	Active TSS	Psoas Muscle	Psoas
28	chr5:58649600-58653600	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr5:58650000-58652000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr5:58650000-58652200	Weak transcription	Fetal Lung	lung
31	chr5:58650200-58651400	Flanking Active TSS	A549	lung
32	chr5:58650400-58651000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:58650400-58651000	Weak transcription	Rectal Smooth Muscle	rectum
34	chr5:58650400-58651400	Enhancers	Stomach Mucosa	stomach
35	chr5:58650400-58651400	Enhancers	HUVEC	blood vessel
36	chr5:58650400-58652600	Weak transcription	Adipose Nuclei	Adipose
37	chr5:58650600-58651200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:58650600-58651200	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:58650800-58651000	Flanking Active TSS	Fetal Heart	heart
40	chr5:58650800-58652400	Weak transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links