Variant report

Variant	rs12516225
Chromosome Location	chr5:94001174-94001175
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10035632	0.80[EUR][1000 genomes]
rs10037228	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10041551	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs10044797	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs10051931	0.92[CEU][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10053484	0.88[CEU][hapmap]
rs10056685	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10058130	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10058618	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs10070258	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10076188	0.88[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs10078049	0.80[EUR][1000 genomes]
rs10078304	0.92[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs10476612	0.88[CEU][hapmap]
rs10476613	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10476615	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs11741678	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs11743258	0.84[ASN][1000 genomes]
rs11949227	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11955373	0.92[CEU][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs12517866	0.88[CEU][hapmap]
rs12518034	0.88[CEU][hapmap]
rs12522312	0.88[CEU][hapmap]
rs13353994	0.87[EUR][1000 genomes]
rs13354061	0.88[EUR][1000 genomes]
rs13358642	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs13361811	0.92[CEU][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13362556	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1376713	0.91[CHB][hapmap]
rs2101898	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs2305391	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs28645132	0.87[EUR][1000 genomes]
rs28787271	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs306573	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs306575	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs3756470	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs55974730	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6873364	0.86[CEU][hapmap]
rs6879307	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755898	0.92[CEU][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7705424	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7725095	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs7725698	0.82[CEU][hapmap]
rs7737779	0.88[CEU][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12516225	ANKRD32	cis	multi-tissue	Pritchard
rs12516225	C5orf36	cis	cerebellum	SCAN
rs12516225	ANKRD32	Cis_1M	lymphoblastoid	RTeQTL
rs12516225	MCTP1	Cis_1M	lymphoblastoid	RTeQTL
rs12516225	ARSK	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:93955800-94027600	Weak transcription	NH-A	brain
2	chr5:93969400-94008400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:93973800-94004200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:93975600-94012000	Weak transcription	Aorta	Aorta
5	chr5:93976800-94025000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:93981000-94012000	Weak transcription	Left Ventricle	heart
7	chr5:93990600-94008200	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:93991200-94049000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:93994200-94010200	Weak transcription	NHEK	skin
10	chr5:93994200-94012000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:93994200-94030800	Weak transcription	Right Ventricle	heart
12	chr5:93994200-94047200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:93994400-94006200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:93994400-94012000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:93994400-94022600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr5:93994400-94025400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr5:93994400-94027600	Weak transcription	Liver	Liver
18	chr5:93994400-94027600	Weak transcription	NHDF-Ad	bronchial
19	chr5:93994400-94029000	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:93994400-94048800	Weak transcription	Small Intestine	intestine
21	chr5:93994600-94007400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:93994600-94026600	Weak transcription	Fetal Kidney	kidney
23	chr5:93994600-94029200	Weak transcription	Brain Anterior Caudate	brain
24	chr5:93994600-94032200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:93995400-94012000	Weak transcription	HepG2	liver
26	chr5:93995400-94024800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:93995600-94009600	Weak transcription	Fetal Brain Female	brain
28	chr5:93995600-94024400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr5:93995600-94033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:93995600-94050400	Weak transcription	Esophagus	oesophagus
31	chr5:93995800-94003000	Weak transcription	A549	lung
32	chr5:93995800-94003200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:93995800-94004600	Strong transcription	Fetal Thymus	thymus
34	chr5:93995800-94010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:93995800-94012000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:93995800-94012000	Weak transcription	HSMM	muscle
37	chr5:93996000-94024000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr5:93996000-94027600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:93996000-94036000	Weak transcription	GM12878-XiMat	blood
40	chr5:93996200-94007400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:93996200-94026600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:93996200-94029800	Weak transcription	Ovary	ovary
43	chr5:93996400-94001600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:93996400-94008000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:93996400-94012000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:93996600-94003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr5:93996600-94012000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr5:93996600-94019200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:93996600-94023000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:93996600-94027800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links