Variant report

Variant	rs12226584
Chromosome Location	chr11:18583258-18583259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10832939	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024691	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11024709	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024718	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11600246	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11603992	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11606375	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12223260	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225251	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16935482	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16935488	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16935538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16935539	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088183	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088184	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292176	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2305167	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3802965	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802966	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4390325	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4417245	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4636650	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756951	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757669	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4757671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757672	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104322	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138729	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56991251	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6486431	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6486435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72876754	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72876774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7483340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7928508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7942733	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv972915	chr11:18571883-18591969	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12226584	LDHC	cis	Nerve Tibial	GTEx
rs12226584	LDHC	cis	Muscle Skeletal	GTEx
rs12226584	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs12226584	LDHC	cis	Adipose Subcutaneous	GTEx
rs12226584	LDHC	cis	lung	GTEx
rs12226584	LDHC	cis	Whole Blood	GTEx
rs12226584	LDHC	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549200-18583400	Weak transcription	Small Intestine	intestine
2	chr11:18549200-18591400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:18549400-18583400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:18549400-18594400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
6	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
8	chr11:18549800-18588200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr11:18549800-18592000	Weak transcription	NHLF	lung
10	chr11:18549800-18594400	Weak transcription	K562	blood
11	chr11:18549800-18600600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:18550600-18591400	Weak transcription	Dnd41	blood
13	chr11:18552600-18601400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr11:18558400-18592200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr11:18559200-18592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr11:18562200-18598200	Weak transcription	Stomach Mucosa	stomach
17	chr11:18563200-18601200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:18564000-18586400	Weak transcription	GM12878-XiMat	blood
20	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr11:18566200-18601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr11:18567200-18594600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:18567400-18601000	Strong transcription	Placenta	Placenta
24	chr11:18567800-18588200	Strong transcription	Adipose Nuclei	Adipose
25	chr11:18568600-18591000	Weak transcription	HMEC	breast
26	chr11:18568600-18600800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:18571200-18585600	Strong transcription	Fetal Stomach	stomach
28	chr11:18571400-18585200	Strong transcription	Fetal Muscle Trunk	muscle
29	chr11:18571800-18601200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:18572000-18588200	Strong transcription	Fetal Muscle Leg	muscle
31	chr11:18573800-18585200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:18574400-18609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:18574600-18592200	Strong transcription	Liver	Liver
34	chr11:18574800-18588600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:18575000-18584000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr11:18575000-18584600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr11:18575000-18588200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:18575000-18609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:18575200-18609200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr11:18575800-18590000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr11:18576200-18590200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:18576600-18596400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:18576800-18594400	Weak transcription	Brain Anterior Caudate	brain
44	chr11:18576800-18599200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:18577400-18599200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr11:18577600-18591400	Weak transcription	HSMMtube	muscle
47	chr11:18577800-18584200	Weak transcription	Colon Smooth Muscle	Colon
48	chr11:18577800-18586000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr11:18578000-18584200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr11:18578000-18584200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links