Variant report

Variant	rs462473
Chromosome Location	chr5:9529809-9529810
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs13178837	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs174863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2458362	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs268544	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs268545	0.96[EUR][1000 genomes]
rs268546	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs268547	0.88[EUR][1000 genomes]
rs268548	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs268549	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs268551	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs268552	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs371458	0.95[EUR][1000 genomes]
rs3756733	0.95[EUR][1000 genomes]
rs375779	0.96[EUR][1000 genomes]
rs377791	0.96[EUR][1000 genomes]
rs382409	0.94[EUR][1000 genomes]
rs390748	0.95[EUR][1000 genomes]
rs398533	0.95[EUR][1000 genomes]
rs406583	0.94[EUR][1000 genomes]
rs420819	0.94[EUR][1000 genomes]
rs435329	0.94[EUR][1000 genomes]
rs439869	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs446573	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs453742	0.96[EUR][1000 genomes]
rs455353	0.94[EUR][1000 genomes]
rs455538	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455757	0.94[EUR][1000 genomes]
rs456058	0.94[EUR][1000 genomes]
rs456400	0.95[EUR][1000 genomes]
rs456837	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs457203	0.94[EUR][1000 genomes]
rs459659	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs459789	0.95[CEU][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs459793	0.96[CEU][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs460887	0.94[EUR][1000 genomes]
rs461321	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs461415	0.94[EUR][1000 genomes]
rs461700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461907	0.94[EUR][1000 genomes]
rs462057	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs462185	0.95[EUR][1000 genomes]
rs462652	0.95[EUR][1000 genomes]
rs463004	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs463029	0.94[EUR][1000 genomes]
rs464267	0.94[EUR][1000 genomes]
rs464616	0.95[EUR][1000 genomes]
rs465205	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs465991	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs466158	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466667	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs466883	0.94[EUR][1000 genomes]
rs630768	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9513000-9532800	Weak transcription	Fetal Stomach	stomach
2	chr5:9513000-9535200	Weak transcription	Aorta	Aorta
3	chr5:9520400-9532800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:9521200-9544400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:9524000-9532800	Weak transcription	NH-A	brain
6	chr5:9524000-9532800	Weak transcription	NHLF	lung
7	chr5:9524000-9533200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:9524000-9534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:9524200-9533000	Weak transcription	Osteobl	bone
10	chr5:9524600-9533200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:9525400-9542000	Weak transcription	Small Intestine	intestine
12	chr5:9526600-9531200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:9527600-9530000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:9527600-9531200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:9528000-9530000	Weak transcription	Fetal Heart	heart
16	chr5:9528400-9530400	Enhancers	Psoas Muscle	Psoas
17	chr5:9528400-9530400	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr5:9528400-9531800	Enhancers	Left Ventricle	heart
19	chr5:9528400-9544200	Weak transcription	Fetal Intestine Small	intestine
20	chr5:9528600-9530200	Enhancers	Right Atrium	heart
21	chr5:9528600-9530400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:9528600-9531800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:9528600-9532000	Enhancers	Fetal Muscle Leg	muscle
24	chr5:9528800-9530200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr5:9528800-9530200	Enhancers	NHDF-Ad	bronchial
26	chr5:9528800-9531000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:9529000-9530200	Enhancers	Liver	Liver
28	chr5:9529000-9530400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr5:9529000-9531800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:9529000-9533000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:9529200-9530200	Enhancers	Adipose Nuclei	Adipose
32	chr5:9529200-9530200	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr5:9529200-9530400	Enhancers	Fetal Muscle Trunk	muscle
34	chr5:9529200-9532000	Enhancers	Right Ventricle	heart
35	chr5:9529400-9530200	Enhancers	Lung	lung
36	chr5:9529400-9530400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:9529600-9533000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr5:9529600-9533200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:9529600-9534000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:9529600-9534200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:9529600-9534600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr5:9529600-9544400	Weak transcription	Pancreas	Pancrea
43	chr5:9529600-9544800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:9529800-9530400	Enhancers	Fetal Brain Male	brain

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