Variant report

Variant	rs7335538
Chromosome Location	chr13:111328728-111328729
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs12429651	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12430171	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12584848	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1853860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1853861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2296655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296656	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2296658	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2296659	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28683030	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2986104	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35206921	0.82[AMR][1000 genomes]
rs365103	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3742193	0.81[JPT][hapmap]
rs3742194	0.81[JPT][hapmap]
rs3742196	0.81[JPT][hapmap]
rs3742201	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs376834	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs388049	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4238278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4268629	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4628819	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4771702	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs4771703	0.85[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4771704	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs4771706	0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4773232	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4773235	0.80[AMR][1000 genomes]
rs544186	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59261018	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66605126	0.88[ASN][1000 genomes]
rs718341	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs72661663	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72661672	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72661683	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7323602	0.81[JPT][hapmap]
rs7328567	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7328764	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7335010	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7336134	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7336283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7399501	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7984290	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7985128	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7985899	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7993933	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8000867	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9521887	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9521888	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9521893	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9521894	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9583520	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs9583523	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9583524	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9588214	0.81[JPT][hapmap]
rs9588232	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9588235	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	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	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
12	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
13	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
14	esv1819597	chr13:111319754-111343888	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv1824622	chr13:111319754-111343888	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv563126	chr13:111328619-111330295	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
17	nsv563127	chr13:111328619-111330354	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7335538	AL139385.1	cis	Muscle Skeletal	GTEx
rs7335538	GRTP1	cis	cerebellum	SCAN
rs7335538	CARKD	cis	parietal	SCAN
rs7335538	EFNB2	cis	cerebellum	SCAN
rs7335538	CARKD	cis	Muscle Skeletal	GTEx
rs7335538	TUBGCP3	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111297800-111336400	Weak transcription	Small Intestine	intestine
2	chr13:111302200-111351400	Weak transcription	Stomach Mucosa	stomach
3	chr13:111310800-111352200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr13:111311600-111352000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr13:111312800-111357400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:111316200-111330600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr13:111316600-111332800	Weak transcription	K562	blood
8	chr13:111319400-111337600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr13:111319800-111348400	Weak transcription	Fetal Brain Male	brain
10	chr13:111319800-111354600	Weak transcription	Fetal Heart	heart
11	chr13:111320200-111339200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:111321800-111328800	Weak transcription	Hela-S3	cervix
13	chr13:111321800-111332800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:111322000-111330000	Weak transcription	NHDF-Ad	bronchial
15	chr13:111322800-111333800	Weak transcription	Fetal Kidney	kidney
16	chr13:111322800-111349600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr13:111327600-111329600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr13:111327800-111329400	Strong transcription	Placenta Amnion	Placenta Amnion
19	chr13:111327800-111331400	Strong transcription	Colonic Mucosa	Colon
20	chr13:111327800-111336000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:111327800-111344200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:111327800-111347400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr13:111327800-111355000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr13:111328000-111328800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:111328000-111328800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr13:111328000-111328800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr13:111328000-111328800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr13:111328000-111328800	ZNF genes & repeats	Esophagus	oesophagus
29	chr13:111328000-111328800	ZNF genes & repeats	Fetal Thymus	thymus
30	chr13:111328000-111329000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr13:111328000-111329000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr13:111328000-111329000	ZNF genes & repeats	Fetal Stomach	stomach
33	chr13:111328000-111329200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr13:111328000-111329200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr13:111328000-111329200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr13:111328000-111329200	Strong transcription	Brain Angular Gyrus	brain
37	chr13:111328000-111329200	Strong transcription	Brain Hippocampus Middle	brain
38	chr13:111328000-111329200	Strong transcription	Colon Smooth Muscle	Colon
39	chr13:111328000-111329200	Strong transcription	A549	lung
40	chr13:111328000-111329200	Strong transcription	NH-A	brain
41	chr13:111328000-111329400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr13:111328000-111329400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr13:111328000-111329400	Flanking Active TSS	GM12878-XiMat	blood
44	chr13:111328000-111329400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr13:111328000-111329600	Strong transcription	Brain Anterior Caudate	brain
46	chr13:111328000-111330400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr13:111328000-111331000	Strong transcription	Fetal Lung	lung
48	chr13:111328000-111331200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr13:111328000-111331600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr13:111328000-111331800	Strong transcription	Brain Inferior Temporal Lobe	brain

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