Variant report

Variant	rs2883562
Chromosome Location	chr4:48859940-48859941
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11727343	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11729065	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11733534	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11734191	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11939889	0.83[EUR][1000 genomes]
rs11943219	0.83[EUR][1000 genomes]
rs12374247	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12512637	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12641022	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13109500	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13119414	0.84[EUR][1000 genomes]
rs13141838	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13149083	0.87[ASN][1000 genomes]
rs13152270	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1463365	0.82[ASN][1000 genomes]
rs1980193	0.84[EUR][1000 genomes]
rs2176460	0.84[EUR][1000 genomes]
rs2289065	0.81[ASN][1000 genomes]
rs2572345	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2572350	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2712156	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2712157	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2712158	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2712159	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34730980	0.82[ASN][1000 genomes]
rs3761729	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4694904	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4694906	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4695400	0.83[EUR][1000 genomes]
rs4695401	0.83[EUR][1000 genomes]
rs4695407	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57797824	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62310934	0.87[ASN][1000 genomes]
rs6447655	0.81[EUR][1000 genomes]
rs6830078	0.83[EUR][1000 genomes]
rs7654032	0.87[ASN][1000 genomes]
rs7657332	0.84[EUR][1000 genomes]
rs7657698	0.83[EUR][1000 genomes]
rs7665209	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7680280	0.81[EUR][1000 genomes]
rs7681070	0.81[EUR][1000 genomes]
rs7687992	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7697522	0.82[EUR][1000 genomes]
rs9291326	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9637562	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9790336	0.81[EUR][1000 genomes]
rs9997920	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv879010	chr4:48794403-49061141	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv1008733	chr4:48827603-48971172	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv427680	chr4:48829607-49660117	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2883562	SLC10A4	cis	lung	GTEx
rs2883562	OCIAD1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48834000-48864600	Weak transcription	Stomach Mucosa	stomach
2	chr4:48835000-48861400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:48835000-48862400	Strong transcription	Fetal Thymus	thymus
4	chr4:48835000-48863000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:48835000-48864400	Strong transcription	HSMM	muscle
6	chr4:48835200-48863200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:48835200-48863800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:48835200-48864200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:48835400-48863200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:48835400-48863400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr4:48835600-48864000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:48835800-48863200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:48836000-48863600	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:48836200-48863600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:48836800-48863200	Strong transcription	Dnd41	blood
16	chr4:48837200-48861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:48838000-48864400	Weak transcription	Esophagus	oesophagus
18	chr4:48838200-48866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:48838400-48863400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr4:48840200-48860000	Weak transcription	Small Intestine	intestine
21	chr4:48841000-48865400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr4:48845400-48863800	Weak transcription	Hela-S3	cervix
23	chr4:48848200-48864600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:48848200-48864600	Weak transcription	Fetal Heart	heart
25	chr4:48848200-48880000	Weak transcription	Brain Substantia Nigra	brain
26	chr4:48851200-48860800	Strong transcription	Placenta	Placenta
27	chr4:48852000-48861800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr4:48852000-48863600	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr4:48852000-48863800	Strong transcription	Fetal Intestine Large	intestine
30	chr4:48852800-48860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:48853200-48864200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr4:48854200-48864200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr4:48854400-48864800	Weak transcription	HSMMtube	muscle
34	chr4:48854400-48865800	Weak transcription	Brain Angular Gyrus	brain
35	chr4:48854600-48862600	Weak transcription	A549	lung
36	chr4:48855600-48863800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:48856000-48862600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr4:48856000-48863200	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:48856200-48860800	Strong transcription	Fetal Stomach	stomach
40	chr4:48856200-48861200	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr4:48856400-48865600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:48856800-48860000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:48856800-48864600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr4:48857000-48860400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:48857000-48860600	Strong transcription	K562	blood
46	chr4:48857000-48862000	Weak transcription	Psoas Muscle	Psoas
47	chr4:48857000-48862400	Weak transcription	NH-A	brain
48	chr4:48857000-48864200	Weak transcription	Fetal Brain Male	brain
49	chr4:48857000-48866000	Weak transcription	Colon Smooth Muscle	Colon
50	chr4:48857600-48860600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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