Variant report

Variant	rs12501643
Chromosome Location	chr4:152071066-152071067
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10009307	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280283	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28593016	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28694456	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36115072	0.81[ASN][1000 genomes]
rs3736502	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3762846	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535764	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6847518	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6858302	0.82[ASN][1000 genomes]
rs7656771	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7675432	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7682480	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7699495	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1017850	chr4:151664438-152071876	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv2763837	chr4:151664438-152071888	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv870257	chr4:151665349-152072867	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv1015387	chr4:151673751-152071876	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv949002	chr4:151693149-152095109	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv1031720	chr4:151708502-152071876	Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv595690	chr4:151788955-152109552	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv1026416	chr4:151847403-152105879	Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
14	nsv1018797	chr4:151913585-152073419	Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
15	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12501643	RPS3A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152025000-152073200	Weak transcription	Stomach Mucosa	stomach
2	chr4:152025200-152073600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:152025200-152085400	Weak transcription	Hela-S3	cervix
4	chr4:152027000-152086600	Weak transcription	Fetal Kidney	kidney
5	chr4:152027200-152095600	Weak transcription	Pancreas	Pancrea
6	chr4:152035600-152072400	Weak transcription	Fetal Brain Male	brain
7	chr4:152040400-152073800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:152043400-152095800	Weak transcription	Placenta	Placenta
9	chr4:152046200-152072400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr4:152047400-152087800	Weak transcription	Psoas Muscle	Psoas
11	chr4:152050600-152087000	Weak transcription	HSMMtube	muscle
12	chr4:152051400-152071200	Weak transcription	Brain Angular Gyrus	brain
13	chr4:152051600-152071600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:152051600-152087200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:152055000-152105800	Weak transcription	Small Intestine	intestine
16	chr4:152059200-152087000	Weak transcription	Fetal Heart	heart
17	chr4:152059400-152074800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr4:152059600-152072400	Strong transcription	Fetal Intestine Small	intestine
19	chr4:152062000-152074800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:152062200-152083800	Weak transcription	Brain Substantia Nigra	brain
21	chr4:152062200-152090000	Weak transcription	Brain Anterior Caudate	brain
22	chr4:152064000-152071800	Strong transcription	HepG2	liver
23	chr4:152064200-152087400	Weak transcription	A549	lung
24	chr4:152065000-152091800	Weak transcription	HMEC	breast
25	chr4:152065400-152087800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr4:152065600-152073800	Weak transcription	Right Atrium	heart
27	chr4:152065600-152089200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:152065800-152086600	Weak transcription	NHLF	lung
29	chr4:152065800-152086800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr4:152066000-152087000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:152066000-152095200	Weak transcription	Esophagus	oesophagus
32	chr4:152066200-152092600	Weak transcription	Colonic Mucosa	Colon
33	chr4:152066200-152095800	Weak transcription	Gastric	stomach
34	chr4:152066400-152095800	Weak transcription	Aorta	Aorta
35	chr4:152066600-152083800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:152066600-152083800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:152067000-152083600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:152067000-152083800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:152067000-152090000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:152067800-152071200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:152068000-152071200	Strong transcription	Adipose Nuclei	Adipose
42	chr4:152068000-152072200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:152068000-152072200	Strong transcription	Fetal Intestine Large	intestine
44	chr4:152068200-152071800	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:152068600-152083800	Weak transcription	NHEK	skin
46	chr4:152069200-152073200	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:152069200-152090000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr4:152069400-152073800	Weak transcription	Lung	lung
49	chr4:152069400-152090000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr4:152069600-152078000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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