Variant report

Variant	rs10875853
Chromosome Location	chr12:49038585-49038586
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49035786..49038249-chr12:49038357..49040344,2	K562	blood:
2	chr12:49033876..49037286-chr12:49037890..49040344,3	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10747554	0.86[ASN][1000 genomes]
rs10783273	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783274	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10783275	0.90[ASN][1000 genomes]
rs10783278	0.97[ASN][1000 genomes]
rs10875850	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875852	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875861	0.92[ASN][1000 genomes]
rs10875862	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875863	0.81[EUR][1000 genomes]
rs1110432	0.87[ASN][1000 genomes]
rs11168657	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168665	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168674	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168697	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11168698	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12299955	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12426435	0.93[ASN][1000 genomes]
rs1316514	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1863541	0.93[ASN][1000 genomes]
rs1895995	0.99[ASN][1000 genomes]
rs2114320	0.88[ASN][1000 genomes]
rs2162317	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277365	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277366	0.95[ASN][1000 genomes]
rs2291728	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2409085	0.98[ASN][1000 genomes]
rs2898087	0.99[ASN][1000 genomes]
rs3209584	0.95[ASN][1000 genomes]
rs35717253	0.99[ASN][1000 genomes]
rs3741628	0.99[ASN][1000 genomes]
rs3741629	0.93[ASN][1000 genomes]
rs3741630	0.97[ASN][1000 genomes]
rs3741632	0.95[ASN][1000 genomes]
rs3803025	0.95[ASN][1000 genomes]
rs3943899	0.93[ASN][1000 genomes]
rs4113946	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4500528	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760735	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760737	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760739	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760740	0.97[ASN][1000 genomes]
rs6580689	0.99[ASN][1000 genomes]
rs6580690	0.99[ASN][1000 genomes]
rs7136021	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7138190	0.99[ASN][1000 genomes]
rs7139236	0.97[ASN][1000 genomes]
rs7299276	0.97[ASN][1000 genomes]
rs7304711	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7305907	0.87[ASN][1000 genomes]
rs7306604	0.91[ASN][1000 genomes]
rs7308699	0.94[ASN][1000 genomes]
rs7308932	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7314665	0.93[ASN][1000 genomes]
rs7954446	0.86[ASN][1000 genomes]
rs7964546	0.90[ASN][1000 genomes]
rs7966065	0.94[ASN][1000 genomes]
rs7973824	0.91[ASN][1000 genomes]
rs7974151	0.85[ASN][1000 genomes]
rs7974625	0.87[ASN][1000 genomes]
rs7975030	0.87[ASN][1000 genomes]
rs9332441	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9634241	0.99[ASN][1000 genomes]
rs9634242	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9634262	0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10875853	KANSL2	cis	Nerve Tibial	GTEx
rs10875853	KANSL2	cis	Skin Sun Exposed Lower leg	GTEx
rs10875853	KANSL2	cis	Thyroid	GTEx
rs10875853	KANSL2	cis	Artery Tibial	GTEx
rs10875853	KANSL2	cis	Esophagus Mucosa	GTEx
rs10875853	KANSL2	cis	lung	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49027600-49046600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:49028200-49045000	Weak transcription	Colonic Mucosa	Colon
3	chr12:49030000-49047200	Weak transcription	Esophagus	oesophagus
4	chr12:49031400-49043800	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr12:49033800-49039000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:49033800-49045200	Weak transcription	Spleen	Spleen
7	chr12:49034400-49042400	Weak transcription	Thymus	Thymus
8	chr12:49034600-49045800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:49034800-49041200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:49034800-49041800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:49034800-49044400	Weak transcription	NHEK	skin
12	chr12:49034800-49045200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:49034800-49045400	Weak transcription	NHDF-Ad	bronchial
14	chr12:49035000-49041200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:49035000-49044400	Weak transcription	Brain Anterior Caudate	brain
16	chr12:49035000-49045600	Weak transcription	K562	blood
17	chr12:49035200-49042200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:49035200-49046800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:49035400-49044600	Weak transcription	HMEC	breast
20	chr12:49035400-49046200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:49035400-49047000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:49035400-49047000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:49035600-49042600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:49035800-49038600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:49035800-49046800	Weak transcription	Gastric	stomach
26	chr12:49035800-49046800	Weak transcription	Ovary	ovary
27	chr12:49036000-49045600	Weak transcription	Right Ventricle	heart
28	chr12:49036200-49039000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:49036200-49041800	Weak transcription	Fetal Stomach	stomach
30	chr12:49036400-49041800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:49036400-49041800	Weak transcription	Fetal Intestine Large	intestine
32	chr12:49036400-49041800	Weak transcription	Lung	lung
33	chr12:49036400-49045000	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:49036400-49045200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:49036400-49045400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr12:49036600-49038600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:49036600-49038600	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:49036600-49038800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:49036600-49038800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:49036600-49038800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr12:49036600-49038800	Strong transcription	Osteobl	bone
42	chr12:49036600-49039000	ZNF genes & repeats	Dnd41	blood
43	chr12:49036600-49041800	Weak transcription	Aorta	Aorta
44	chr12:49036600-49044200	Weak transcription	Fetal Thymus	thymus
45	chr12:49036600-49044800	Weak transcription	Brain Hippocampus Middle	brain
46	chr12:49036600-49045000	Weak transcription	Left Ventricle	heart
47	chr12:49036600-49045200	Weak transcription	Brain Substantia Nigra	brain
48	chr12:49036800-49038600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:49036800-49038600	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:49036800-49039000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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