Variant report

Variant	rs17118208
Chromosome Location	chr12:56381301-56381302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56379655..56383410-chr12:56384444..56387203,3	K562	blood:
2	chr12:56374509..56377876-chr12:56378080..56382114,4	MCF-7	breast:
3	chr12:56380547..56382157-chr12:56387851..56389838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111540	Chromatin interaction
ENSG00000237493	Chromatin interaction
ENSG00000255990	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1045435	0.88[CEU][hapmap];0.98[EUR][1000 genomes]
rs11171713	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11171714	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11171715	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11550558	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs12099979	0.87[AMR][1000 genomes]
rs12309895	0.85[YRI][hapmap]
rs12810011	0.81[AMR][1000 genomes]
rs12815302	0.93[AMR][1000 genomes]
rs12815387	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs12815488	0.93[AMR][1000 genomes]
rs12817765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12831468	0.93[AMR][1000 genomes]
rs12831884	0.88[CEU][hapmap]
rs1689511	0.88[CEU][hapmap]
rs1701706	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs17118206	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17118262	0.93[AMR][1000 genomes]
rs2069391	1.00[CHD][hapmap];0.90[GIH][hapmap]
rs2456972	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs2658479	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs3213122	1.00[CHD][hapmap];0.90[GIH][hapmap]
rs34071823	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34228181	0.87[AMR][1000 genomes]
rs34273234	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34303864	0.93[AMR][1000 genomes]
rs34406511	0.81[AMR][1000 genomes]
rs34485293	0.81[AMR][1000 genomes]
rs34602183	0.81[AMR][1000 genomes]
rs34650555	0.81[AMR][1000 genomes]
rs34921584	0.81[AMR][1000 genomes]
rs34962186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35485002	0.81[AMR][1000 genomes]
rs4759022	0.85[CEU][hapmap]
rs67594137	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71447768	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459326	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459327	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459334	0.93[AMR][1000 genomes]
rs71459336	0.81[AMR][1000 genomes]
rs71459339	0.87[AMR][1000 genomes]
rs7298818	0.81[AMR][1000 genomes]
rs772922	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs772923	0.88[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs7977537	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17118208	SUOX	cis	Thyroid	GTEx
rs17118208	LOC644166///LOC644191///LOC728937///RPS26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56368600-56383200	Weak transcription	Gastric	stomach
2	chr12:56369000-56383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:56369200-56383600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:56369200-56384600	Weak transcription	Psoas Muscle	Psoas
5	chr12:56369400-56383400	Weak transcription	Pancreas	Pancrea
6	chr12:56369400-56384200	Weak transcription	Fetal Brain Male	brain
7	chr12:56369400-56389400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:56369800-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr12:56370000-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr12:56370000-56389600	Strong transcription	Fetal Thymus	thymus
11	chr12:56370200-56389600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr12:56370400-56385000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:56370400-56388400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:56370600-56383200	Weak transcription	HepG2	liver
15	chr12:56370600-56383400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:56370600-56388200	Strong transcription	Dnd41	blood
17	chr12:56370600-56389600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:56370800-56383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:56371400-56381800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:56371400-56389600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:56371600-56383400	Weak transcription	Colon Smooth Muscle	Colon
22	chr12:56371600-56388800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:56371800-56383400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:56372400-56390000	Strong transcription	Placenta	Placenta
25	chr12:56372800-56386200	Strong transcription	Fetal Intestine Large	intestine
26	chr12:56372800-56389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:56372800-56389600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:56372800-56389600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:56373200-56386600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:56373400-56389400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:56373400-56389600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:56373600-56383400	Weak transcription	Stomach Mucosa	stomach
33	chr12:56373600-56388600	Strong transcription	Liver	Liver
34	chr12:56373800-56386000	Strong transcription	Fetal Intestine Small	intestine
35	chr12:56374000-56388600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr12:56374000-56389600	Strong transcription	Fetal Stomach	stomach
37	chr12:56374200-56388800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:56375400-56381600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:56375600-56381800	Weak transcription	Brain Angular Gyrus	brain
40	chr12:56375600-56381800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:56375600-56382800	Weak transcription	A549	lung
42	chr12:56375600-56383000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr12:56375600-56384400	Weak transcription	Hela-S3	cervix
44	chr12:56375800-56390600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr12:56376000-56389600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:56376600-56388200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:56376600-56388800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr12:56376600-56389600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:56376800-56383400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr12:56377000-56389400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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