Variant report

Variant	rs11171713
Chromosome Location	chr12:56374803-56374804
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56222612..56225517-chr12:56372520..56376647,5	MCF-7	breast:
2	chr12:56320862..56327055-chr12:56370927..56377943,9	MCF-7	breast:
3	chr12:56350213..56352992-chr12:56373952..56376823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135392	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000185664	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1045435	0.89[CEU][hapmap];0.98[EUR][1000 genomes]
rs11171714	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11171715	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11550558	1.00[CEU][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]
rs12815488	0.93[AMR][1000 genomes]
rs12817765	0.82[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	0.89[CEU][hapmap]
rs1701706	0.88[CEU][hapmap]
rs17118206	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17118208	1.00[CEU][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]
rs2456972	0.88[CEU][hapmap]
rs2658479	0.88[CEU][hapmap]
rs34071823	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34228181	0.87[AMR][1000 genomes]
rs34273234	0.86[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	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71447768	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459326	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71459327	1.00[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]
rs772923	0.88[CEU][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11171713	SUOX	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56368600-56375400	Weak transcription	Lung	lung
2	chr12:56368600-56383200	Weak transcription	Gastric	stomach
3	chr12:56368800-56379000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:56369000-56383600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:56369200-56375000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:56369200-56375200	Weak transcription	A549	lung
7	chr12:56369200-56376200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:56369200-56376200	Weak transcription	NHDF-Ad	bronchial
9	chr12:56369200-56379000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:56369200-56380000	Weak transcription	Right Ventricle	heart
11	chr12:56369200-56380400	Weak transcription	Aorta	Aorta
12	chr12:56369200-56383600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr12:56369200-56384600	Weak transcription	Psoas Muscle	Psoas
14	chr12:56369400-56375200	Weak transcription	Fetal Brain Female	brain
15	chr12:56369400-56375200	Weak transcription	Fetal Kidney	kidney
16	chr12:56369400-56379400	Strong transcription	Fetal Muscle Leg	muscle
17	chr12:56369400-56381000	Weak transcription	Small Intestine	intestine
18	chr12:56369400-56383400	Weak transcription	Pancreas	Pancrea
19	chr12:56369400-56384200	Weak transcription	Fetal Brain Male	brain
20	chr12:56369400-56389400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:56369800-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:56370000-56375200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:56370000-56376400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:56370000-56389600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:56370000-56389600	Strong transcription	Fetal Thymus	thymus
26	chr12:56370200-56375400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:56370200-56375400	Strong transcription	NHEK	skin
28	chr12:56370200-56389600	Strong transcription	Fetal Muscle Trunk	muscle
29	chr12:56370400-56375000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:56370400-56385000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:56370400-56388400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:56370600-56375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:56370600-56376200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:56370600-56376400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:56370600-56379000	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:56370600-56383200	Weak transcription	HepG2	liver
37	chr12:56370600-56383400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:56370600-56388200	Strong transcription	Dnd41	blood
39	chr12:56370600-56389600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:56370800-56375200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr12:56370800-56376600	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:56370800-56378600	Weak transcription	Brain Substantia Nigra	brain
43	chr12:56370800-56383400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:56371000-56377600	Weak transcription	Left Ventricle	heart
45	chr12:56371000-56379600	Weak transcription	Right Atrium	heart
46	chr12:56371200-56375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:56371400-56375800	Strong transcription	NHLF	lung
48	chr12:56371400-56381800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:56371400-56389600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:56371600-56375200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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