Variant report

Variant	rs61512578
Chromosome Location	chr12:104218838-104218839
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104218296..104220152-chr12:104227308..104229247,2	K562	blood:
2	chr12:104213266..104215424-chr12:104217652..104220137,3	MCF-7	breast:
3	chr12:104214519..104222192-chr12:104231005..104236989,8	K562	blood:
4	chr12:104218540..104220956-chr12:104233620..104235527,2	MCF-7	breast:
5	chr12:104208479..104212455-chr12:104217163..104218930,3	MCF-7	breast:

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

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1057892	0.84[EUR][1000 genomes]
rs11111802	0.88[ASN][1000 genomes]
rs12422418	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12422615	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12422701	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12423476	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12423889	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12423912	0.87[EUR][1000 genomes]
rs12423994	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12424929	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12424984	0.90[EUR][1000 genomes]
rs12425283	0.87[EUR][1000 genomes]
rs12425537	1.00[AFR][1000 genomes]
rs1437505	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1550207	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1550208	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034593	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs17034620	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17034642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17794246	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2289258	0.83[EUR][1000 genomes]
rs3812802	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55724382	0.84[EUR][1000 genomes]
rs55736751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55810720	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs55932227	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55949441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55987022	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55993375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56123042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56143748	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56147174	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56255894	0.90[EUR][1000 genomes]
rs56314567	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56403068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57173983	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59651914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59716163	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60378307	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61748068	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs7295408	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7314150	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7485127	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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:51 , 50 per page) page: 1 2

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	chr12:104214800-104219400	Weak transcription	Ovary	ovary
8	chr12:104215000-104219800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr12:104215200-104221800	Weak transcription	Aorta	Aorta
10	chr12:104215200-104226000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:104215200-104227600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:104215400-104221200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:104215400-104221600	Weak transcription	HepG2	liver
16	chr12:104215400-104221800	Weak transcription	Brain Angular Gyrus	brain
17	chr12:104215400-104223400	Enhancers	Rectal Smooth Muscle	rectum
18	chr12:104215800-104219400	Weak transcription	A549	lung
19	chr12:104215800-104221600	Weak transcription	NHLF	lung
20	chr12:104216400-104221400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:104216400-104221600	Weak transcription	HSMM	muscle
22	chr12:104216600-104219400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:104216600-104221600	Weak transcription	HMEC	breast
24	chr12:104216600-104221800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:104216600-104221800	Weak transcription	NHEK	skin
26	chr12:104216600-104227800	Weak transcription	NH-A	brain
27	chr12:104217000-104221400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:104217400-104219000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:104217600-104219000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:104217600-104219600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:104217800-104222000	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:104218000-104220200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:104218200-104219400	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:104218200-104220000	Enhancers	Stomach Smooth Muscle	stomach
35	chr12:104218200-104220400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr12:104218400-104219000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:104218400-104219800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:104218400-104220200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:104218400-104221600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr12:104218400-104221800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:104218400-104224800	Weak transcription	K562	blood
42	chr12:104218400-104233000	Weak transcription	Gastric	stomach
43	chr12:104218400-104233400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:104218600-104219000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:104218600-104219000	Enhancers	Osteobl	bone
46	chr12:104218600-104220600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:104218800-104219000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:104218800-104219400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:104218800-104219400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:104218800-104227400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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