Variant report

Variant	rs426702
Chromosome Location	chr13:111308046-111308047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:111307316-111308221	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111304729..111307376-chr13:111307813..111310341,2	K562	blood:

Variant related genes	Relation type
CARS2	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs2251314	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2477917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2478465	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2478466	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2765343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2766497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2766498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2986085	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986086	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986087	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986090	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2986325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2986326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs366571	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368860	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs379114	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs379140	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs384385	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs388532	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389189	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs393029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs396523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs409996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411771	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418321	0.94[AFR][1000 genomes]
rs422087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs424376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs424725	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs433080	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436283	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445490	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9588224	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS 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	216 gene(s)	inside rSNPs	diseases
2	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
3	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
10	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
11	nsv456120	chr13:111280002-111309617	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
12	nsv563125	chr13:111280002-111309617	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
13	nsv1042232	chr13:111282123-111348475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
14	nsv901013	chr13:111291192-111340342	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
15	nsv901014	chr13:111302922-111380684	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	197 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs426702	AL139385.1	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111280800-111328600	Weak transcription	Psoas Muscle	Psoas
2	chr13:111282000-111309600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr13:111282800-111310000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr13:111286200-111308400	Strong transcription	Dnd41	blood
5	chr13:111286400-111308200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:111286800-111309400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:111287400-111310200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:111287800-111309800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr13:111289400-111312000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr13:111289600-111310000	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr13:111293400-111314800	Weak transcription	HUVEC	blood vessel
12	chr13:111294000-111311800	Weak transcription	Fetal Kidney	kidney
13	chr13:111296000-111311600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr13:111296600-111311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr13:111296800-111310000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr13:111296800-111310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr13:111297200-111310200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr13:111297200-111313800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr13:111297600-111310000	Strong transcription	Fetal Intestine Small	intestine
20	chr13:111297600-111314400	Strong transcription	Fetal Intestine Large	intestine
21	chr13:111297800-111308200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr13:111297800-111308400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr13:111297800-111308400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr13:111297800-111308400	Strong transcription	Lung	lung
25	chr13:111297800-111310600	Strong transcription	Fetal Stomach	stomach
26	chr13:111297800-111311400	Strong transcription	Fetal Muscle Leg	muscle
27	chr13:111297800-111317200	Weak transcription	Colon Smooth Muscle	Colon
28	chr13:111297800-111336400	Weak transcription	Small Intestine	intestine
29	chr13:111298000-111308400	Strong transcription	Stomach Smooth Muscle	stomach
30	chr13:111298000-111308800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr13:111298000-111309000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr13:111298000-111310200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr13:111298000-111320400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr13:111298200-111309000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr13:111298200-111309600	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr13:111298200-111309800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr13:111298400-111310000	Weak transcription	A549	lung
38	chr13:111299400-111308200	Strong transcription	Adipose Nuclei	Adipose
39	chr13:111300600-111308800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr13:111300800-111308200	Strong transcription	Primary T cells from cord blood	blood
41	chr13:111300800-111308800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr13:111301200-111308400	Strong transcription	Thymus	Thymus
43	chr13:111301200-111315600	Weak transcription	K562	blood
44	chr13:111301200-111322800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr13:111301400-111308800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr13:111301600-111311400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:111301600-111322800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:111301600-111324400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:111301800-111313600	Weak transcription	Fetal Brain Male	brain
50	chr13:111302000-111322800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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