Variant report

Variant	rs56671180
Chromosome Location	chr12:50809831-50809832
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50803668..50806425-chr12:50809332..50811405,2	K562	blood:
2	chr12:50793235..50796567-chr12:50807744..50811456,6	K562	blood:
3	chr12:50720749..50723312-chr12:50808337..50810670,2	MCF-7	breast:
4	chr12:50794108..50796567-chr12:50808356..50811014,3	K562	blood:
5	chr12:50801905..50804539-chr12:50808374..50809962,2	K562	blood:

Variant related genes	Relation type
ENSG00000161813	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10506293	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747580	0.87[ASN][1000 genomes]
rs10747581	0.87[ASN][1000 genomes]
rs10783362	0.95[ASN][1000 genomes]
rs10783368	0.85[EUR][1000 genomes]
rs10876034	0.93[ASN][1000 genomes]
rs10876048	0.85[EUR][1000 genomes]
rs10876054	0.85[EUR][1000 genomes]
rs11169408	0.81[ASN][1000 genomes]
rs11169422	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169427	0.87[ASN][1000 genomes]
rs11169440	0.93[ASN][1000 genomes]
rs12099511	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12099615	0.90[EUR][1000 genomes]
rs12296379	0.90[EUR][1000 genomes]
rs12307602	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12320201	0.85[EUR][1000 genomes]
rs12578525	0.95[ASN][1000 genomes]
rs13328926	0.90[EUR][1000 genomes]
rs1402693	0.90[EUR][1000 genomes]
rs17119774	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17119778	0.89[ASN][1000 genomes]
rs17124672	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17531020	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1996750	0.90[EUR][1000 genomes]
rs2252595	0.81[EUR][1000 genomes]
rs2684902	0.85[EUR][1000 genomes]
rs2684906	0.85[EUR][1000 genomes]
rs28414775	0.90[EUR][1000 genomes]
rs28479152	0.90[EUR][1000 genomes]
rs2947617	0.85[EUR][1000 genomes]
rs4129355	0.85[EUR][1000 genomes]
rs4238104	0.95[ASN][1000 genomes]
rs4257057	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4298982	0.93[ASN][1000 genomes]
rs4306347	0.90[EUR][1000 genomes]
rs4351895	0.95[ASN][1000 genomes]
rs4450234	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4517607	0.90[EUR][1000 genomes]
rs4562889	0.81[EUR][1000 genomes]
rs4768877	0.86[ASN][1000 genomes]
rs4768878	0.93[ASN][1000 genomes]
rs4768879	0.95[ASN][1000 genomes]
rs4768880	0.93[ASN][1000 genomes]
rs4768887	0.85[EUR][1000 genomes]
rs4768928	0.85[ASN][1000 genomes]
rs4768936	0.86[ASN][1000 genomes]
rs56150799	0.81[AMR][1000 genomes]
rs56753963	0.90[EUR][1000 genomes]
rs56989201	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57283487	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57293958	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57512759	0.90[EUR][1000 genomes]
rs57578212	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57811009	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57828015	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58500867	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58869591	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58888905	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58915267	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58916974	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58943330	0.90[EUR][1000 genomes]
rs59163743	0.85[AMR][1000 genomes]
rs59194948	0.90[EUR][1000 genomes]
rs59683461	0.90[EUR][1000 genomes]
rs59696942	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59968707	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60010359	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60198651	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60201334	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60239257	0.90[EUR][1000 genomes]
rs60242613	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60396677	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60420087	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60494920	0.90[EUR][1000 genomes]
rs60610745	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60743903	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60908906	0.90[EUR][1000 genomes]
rs61578731	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580745	0.81[AMR][1000 genomes]
rs6580753	0.95[ASN][1000 genomes]
rs6580754	0.94[ASN][1000 genomes]
rs7131993	0.85[EUR][1000 genomes]
rs7133488	0.89[ASN][1000 genomes]
rs7135159	0.85[ASN][1000 genomes]
rs7135222	0.85[EUR][1000 genomes]
rs7138063	0.93[ASN][1000 genomes]
rs7295610	0.89[ASN][1000 genomes]
rs7296212	0.86[ASN][1000 genomes]
rs7299321	0.89[ASN][1000 genomes]
rs7301125	0.85[EUR][1000 genomes]
rs7302749	0.85[EUR][1000 genomes]
rs7304017	0.93[ASN][1000 genomes]
rs7304262	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306387	0.90[EUR][1000 genomes]
rs74090120	0.86[AMR][1000 genomes]
rs7487645	0.90[EUR][1000 genomes]
rs7953880	0.90[EUR][1000 genomes]
rs7955176	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7955310	0.85[EUR][1000 genomes]
rs7957033	0.95[ASN][1000 genomes]
rs7965165	0.87[ASN][1000 genomes]
rs7974480	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7978443	0.90[EUR][1000 genomes]
rs7978625	0.89[ASN][1000 genomes]
rs7979184	0.84[EUR][1000 genomes]
rs951591	0.90[EUR][1000 genomes]
rs9634264	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS 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	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
7	nsv469376	chr12:50792846-50856613	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	nsv558841	chr12:50792846-50856613	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
9	nsv470291	chr12:50792846-50858820	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50795400-50819400	Weak transcription	Spleen	Spleen
2	chr12:50796000-50812400	Weak transcription	Esophagus	oesophagus
3	chr12:50796000-50819400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:50796800-50810000	Weak transcription	Aorta	Aorta
5	chr12:50796800-50823200	Weak transcription	HSMMtube	muscle
6	chr12:50796800-50824000	Weak transcription	Fetal Brain Female	brain
7	chr12:50796800-50832600	Weak transcription	Brain Substantia Nigra	brain
8	chr12:50797000-50821800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:50797000-50822200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:50797000-50822600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:50797200-50810400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr12:50797200-50823800	Weak transcription	NH-A	brain
13	chr12:50797600-50810000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:50797600-50810200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:50797600-50811200	Weak transcription	Fetal Heart	heart
16	chr12:50797600-50812000	Weak transcription	HMEC	breast
17	chr12:50797600-50815600	Weak transcription	Brain Germinal Matrix	brain
18	chr12:50797600-50822800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:50797600-50826200	Weak transcription	NHDF-Ad	bronchial
20	chr12:50797600-50826800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:50797600-50829600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:50798200-50819400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:50798400-50810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:50798400-50810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:50798400-50812000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:50798400-50822400	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:50798400-50824000	Weak transcription	Fetal Kidney	kidney
28	chr12:50799000-50810200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:50799000-50812000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr12:50799000-50818800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:50799600-50812000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:50802400-50812000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:50803200-50823200	Weak transcription	Small Intestine	intestine
34	chr12:50805000-50812800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:50805600-50814600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:50805800-50818600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:50806400-50813000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr12:50806400-50819200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr12:50807200-50819400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:50807200-50824000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:50807400-50810600	Strong transcription	HepG2	liver
42	chr12:50807400-50822600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:50807600-50810000	Weak transcription	Brain Anterior Caudate	brain
44	chr12:50808000-50810400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:50808000-50813600	Strong transcription	Fetal Intestine Small	intestine
46	chr12:50808200-50810400	Strong transcription	Dnd41	blood
47	chr12:50808200-50824000	Weak transcription	Brain Angular Gyrus	brain
48	chr12:50808400-50810000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:50808400-50812200	Weak transcription	Psoas Muscle	Psoas
50	chr12:50808400-50812400	Strong transcription	Fetal Thymus	thymus

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