Variant report

Variant	rs40444
Chromosome Location	chr5:58593451-58593452
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1457146	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs149106	0.95[ASN][1000 genomes]
rs153948	0.92[ASN][1000 genomes]
rs153949	0.95[ASN][1000 genomes]
rs171729	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs255633	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs255649	0.82[EUR][1000 genomes]
rs255650	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs255655	0.96[CEU][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256750	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs256752	0.92[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26710	0.83[YRI][hapmap]
rs26714	0.83[YRI][hapmap]
rs26715	0.86[YRI][hapmap]
rs27170	0.88[CEU][hapmap]
rs27178	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs27183	0.88[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs27184	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs27395	0.94[CHB][hapmap];0.93[ASN][1000 genomes]
rs27670	0.86[YRI][hapmap]
rs27695	0.86[YRI][hapmap]
rs34739	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs37353	0.92[CEU][hapmap]

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	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58583600-58596400	Weak transcription	Esophagus	oesophagus
2	chr5:58584000-58596400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:58590200-58594800	Weak transcription	Gastric	stomach
4	chr5:58591200-58595600	Enhancers	Fetal Heart	heart
5	chr5:58591600-58596400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:58591600-58597600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:58592400-58593600	Active TSS	Right Atrium	heart
8	chr5:58592400-58593800	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr5:58592400-58593800	Enhancers	Fetal Intestine Large	intestine
10	chr5:58592400-58594000	Enhancers	Fetal Intestine Small	intestine
11	chr5:58592600-58593600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr5:58592600-58593600	Weak transcription	Small Intestine	intestine
13	chr5:58592800-58597800	Weak transcription	Left Ventricle	heart
14	chr5:58593000-58593800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr5:58593000-58594000	Weak transcription	Psoas Muscle	Psoas
16	chr5:58593000-58594000	Enhancers	Stomach Mucosa	stomach
17	chr5:58593000-58594800	Weak transcription	Colonic Mucosa	Colon
18	chr5:58593000-58611200	Weak transcription	Right Ventricle	heart
19	chr5:58593200-58593800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:58593200-58593800	Flanking Active TSS	NHEK	skin
21	chr5:58593200-58594000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:58593200-58594800	Weak transcription	Fetal Kidney	kidney
23	chr5:58593200-58594800	Weak transcription	Fetal Muscle Leg	muscle
24	chr5:58593200-58595200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr5:58593200-58595400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:58593200-58595400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:58593200-58595600	Enhancers	Colon Smooth Muscle	Colon
28	chr5:58593200-58596600	Weak transcription	HSMMtube	muscle
29	chr5:58593200-58598200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:58593200-58612600	Weak transcription	Fetal Lung	lung
31	chr5:58593200-58613400	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:58593400-58593600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:58593400-58593600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:58593400-58593600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:58593400-58593600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:58593400-58593600	Enhancers	Osteobl	bone
37	chr5:58593400-58593800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr5:58593400-58593800	Enhancers	Liver	Liver
39	chr5:58593400-58593800	Enhancers	Brain Anterior Caudate	brain
40	chr5:58593400-58593800	Enhancers	Brain Hippocampus Middle	brain
41	chr5:58593400-58593800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:58593400-58593800	Enhancers	Brain Substantia Nigra	brain
43	chr5:58593400-58593800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr5:58593400-58593800	Flanking Active TSS	A549	lung
45	chr5:58593400-58594200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr5:58593400-58594400	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr5:58593400-58594400	Active TSS	Hela-S3	cervix
48	chr5:58593400-58594800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr5:58593400-58595200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr5:58593400-58595400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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