Variant report

Variant	rs13362556
Chromosome Location	chr5:93995180-93995181
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10035632	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10035650	1.00[CHB][hapmap]
rs10037228	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039801	1.00[CHB][hapmap]
rs10041262	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10041843	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10043779	1.00[CHB][hapmap]
rs10044797	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10051931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10053484	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056685	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10058130	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10059194	1.00[CHB][hapmap]
rs10061737	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10062248	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10070258	0.95[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10076188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10076461	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078049	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10078304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10476612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10476613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10476615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11949227	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11955373	1.00[CEU][hapmap];0.91[YRI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11960129	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12516225	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12517866	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518034	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522312	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169956	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13353994	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13354061	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13358642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17083818	1.00[CHB][hapmap]
rs28645132	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28787271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs306573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs306575	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4869218	0.90[EUR][1000 genomes]
rs55974730	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6862592	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873364	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6879307	0.89[EUR][1000 genomes]
rs755898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705424	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7725095	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7725698	0.88[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7731360	0.82[EUR][1000 genomes]
rs7737779	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758002	chr5:93765205-94042201	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759354	chr5:93765205-94042201	Active TSS ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv462254	chr5:93956937-94056825	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv598953	chr5:93956937-94056825	ZNF genes & repeats Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv882386	chr5:93973177-94008969	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13362556	ANKRD32	cis	multi-tissue	Pritchard
rs13362556	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs13362556	MCTP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93955000-93995400	Weak transcription	Gastric	stomach
2	chr5:93955800-93995400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:93955800-94027600	Weak transcription	NH-A	brain
4	chr5:93963800-93995800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:93964600-93995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:93968000-93995200	Weak transcription	HSMM	muscle
7	chr5:93969400-94008400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:93971400-93995400	Weak transcription	Spleen	Spleen
9	chr5:93973800-93995200	Weak transcription	Lung	lung
10	chr5:93973800-94004200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:93974200-93995400	Weak transcription	Ovary	ovary
12	chr5:93974400-93995200	Weak transcription	Thymus	Thymus
13	chr5:93975600-93995200	Weak transcription	Esophagus	oesophagus
14	chr5:93975600-93995200	Weak transcription	Fetal Stomach	stomach
15	chr5:93975600-94012000	Weak transcription	Aorta	Aorta
16	chr5:93976800-94025000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr5:93977800-93995400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:93981000-94012000	Weak transcription	Left Ventricle	heart
19	chr5:93982600-93995400	Weak transcription	Pancreas	Pancrea
20	chr5:93987600-93995400	Strong transcription	Fetal Thymus	thymus
21	chr5:93988400-93996200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:93988600-93997800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:93988800-93995800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:93989000-93995600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:93989800-93995200	Weak transcription	Fetal Intestine Small	intestine
26	chr5:93990200-93995800	ZNF genes & repeats	A549	lung
27	chr5:93990600-93995600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
28	chr5:93990600-93995800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr5:93990600-93996200	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr5:93990600-94008200	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:93991200-93995400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:93991200-93995400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr5:93992600-93995400	Weak transcription	Placenta	Placenta
35	chr5:93992800-93998000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:93993000-93995400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
37	chr5:93993000-93995600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
38	chr5:93993000-93995600	ZNF genes & repeats	Fetal Lung	lung
39	chr5:93993200-93995200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
40	chr5:93993200-93995400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:93993200-93995600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
42	chr5:93993400-93995400	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr5:93993600-93996000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr5:93994000-93999000	Weak transcription	Osteobl	bone
45	chr5:93994200-93995200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:93994200-93995200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr5:93994200-93999600	Weak transcription	Adipose Nuclei	Adipose
48	chr5:93994200-93999800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:93994200-94010200	Weak transcription	NHEK	skin
50	chr5:93994200-94012000	Weak transcription	Rectal Mucosa Donor 29	rectum

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