Variant report

Variant	rs59509226
Chromosome Location	chr12:104218426-104218427
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104211016..104214804-chr12:104214822..104218776,4	K562	blood:
2	chr12:104218296..104220152-chr12:104227308..104229247,2	K562	blood:
3	chr12:104213266..104215424-chr12:104217652..104220137,3	MCF-7	breast:
4	chr12:104214519..104222192-chr12:104231005..104236989,8	K562	blood:
5	chr12:104208479..104212455-chr12:104217163..104218930,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257327	Chromatin interaction
ENSG00000257754	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10861110	0.84[ASN][1000 genomes]
rs10861114	0.82[ASN][1000 genomes]
rs10861116	0.82[ASN][1000 genomes]
rs10861117	0.81[ASN][1000 genomes]
rs11111780	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11111806	0.81[ASN][1000 genomes]
rs11111807	0.81[ASN][1000 genomes]
rs12299784	0.82[ASN][1000 genomes]
rs12312058	0.84[ASN][1000 genomes]
rs12320424	0.82[ASN][1000 genomes]
rs1370782	0.91[ASN][1000 genomes]
rs1370783	0.95[ASN][1000 genomes]
rs17034527	0.88[ASN][1000 genomes]
rs17034633	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034635	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034657	0.82[ASN][1000 genomes]
rs4964571	0.90[ASN][1000 genomes]
rs4964574	0.81[ASN][1000 genomes]
rs4964605	0.84[ASN][1000 genomes]
rs57412476	0.88[ASN][1000 genomes]
rs57498429	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57739230	0.84[ASN][1000 genomes]
rs60828015	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6539102	0.90[ASN][1000 genomes]
rs7132446	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135803	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295408	0.97[AFR][1000 genomes]
rs7314150	0.92[AFR][1000 genomes]
rs884394	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs934844	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104196400-104221800	Weak transcription	Brain Anterior Caudate	brain
2	chr12:104208200-104221800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:104208200-104223200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:104208200-104227800	Weak transcription	Pancreas	Pancrea
5	chr12:104208600-104221200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:104208800-104227600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:104213800-104218800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:104214800-104219400	Weak transcription	Ovary	ovary
9	chr12:104215000-104219800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr12:104215200-104218600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:104215200-104218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:104215200-104221800	Weak transcription	Aorta	Aorta
13	chr12:104215200-104226000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:104215200-104227600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:104215400-104218600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr12:104215400-104221200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:104215400-104221600	Weak transcription	HepG2	liver
20	chr12:104215400-104221800	Weak transcription	Brain Angular Gyrus	brain
21	chr12:104215400-104223400	Enhancers	Rectal Smooth Muscle	rectum
22	chr12:104215800-104219400	Weak transcription	A549	lung
23	chr12:104215800-104221600	Weak transcription	NHLF	lung
24	chr12:104216400-104221400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:104216400-104221600	Weak transcription	HSMM	muscle
26	chr12:104216600-104219400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:104216600-104221600	Weak transcription	HMEC	breast
28	chr12:104216600-104221800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:104216600-104221800	Weak transcription	NHEK	skin
30	chr12:104216600-104227800	Weak transcription	NH-A	brain
31	chr12:104216800-104218600	Weak transcription	Osteobl	bone
32	chr12:104217000-104221400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:104217400-104219000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:104217600-104218800	Enhancers	Psoas Muscle	Psoas
35	chr12:104217600-104219000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:104217600-104219600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:104217800-104218600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr12:104217800-104222000	Weak transcription	Fetal Muscle Leg	muscle
39	chr12:104218000-104220200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:104218200-104219400	Weak transcription	Colon Smooth Muscle	Colon
41	chr12:104218200-104220000	Enhancers	Stomach Smooth Muscle	stomach
42	chr12:104218200-104220400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr12:104218400-104219000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:104218400-104219800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr12:104218400-104220200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:104218400-104221600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr12:104218400-104221800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:104218400-104224800	Weak transcription	K562	blood
49	chr12:104218400-104233000	Weak transcription	Gastric	stomach
50	chr12:104218400-104233400	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links