Variant report

Variant	rs865490
Chromosome Location	chr12:51204149-51204150
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51156449..51158602-chr12:51202622..51204712,2	K562	blood:
2	chr12:51203453..51205584-chr12:51379862..51382375,2	MCF-7	breast:
3	chr12:51179438..51182295-chr12:51203599..51205649,2	MCF-7	breast:
4	chr12:51202962..51206871-chr12:51207911..51210941,4	K562	blood:
5	chr12:51159281..51161379-chr12:51202424..51204535,2	K562	blood:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10506296	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10735827	0.96[ASN][1000 genomes]
rs10747590	0.87[ASN][1000 genomes]
rs10747592	0.96[ASN][1000 genomes]
rs10747593	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10783388	0.96[ASN][1000 genomes]
rs10876082	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876083	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876085	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876088	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876091	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169551	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11169553	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169556	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12099615	0.81[EUR][1000 genomes]
rs12320201	0.86[EUR][1000 genomes]
rs1402693	0.81[EUR][1000 genomes]
rs1521515	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1521517	0.86[EUR][1000 genomes]
rs1561422	0.96[ASN][1000 genomes]
rs17124888	0.90[EUR][1000 genomes]
rs17124907	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1815010	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1996750	0.81[EUR][1000 genomes]
rs2246840	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2252595	0.82[EUR][1000 genomes]
rs2684886	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2684890	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2684891	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2684902	0.86[EUR][1000 genomes]
rs2684906	0.86[EUR][1000 genomes]
rs2700486	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2947617	0.86[EUR][1000 genomes]
rs3803181	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3825401	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4143663	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768862	0.91[ASN][1000 genomes]
rs4768909	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768915	0.95[EUR][1000 genomes]
rs4768920	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56753963	0.81[EUR][1000 genomes]
rs56818625	0.90[EUR][1000 genomes]
rs57328764	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58301497	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58943330	0.81[EUR][1000 genomes]
rs59194948	0.81[EUR][1000 genomes]
rs59284993	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60908906	0.81[EUR][1000 genomes]
rs61926300	0.86[ASN][1000 genomes]
rs6580766	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580767	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580768	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6580770	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132443	0.90[EUR][1000 genomes]
rs7135222	0.86[EUR][1000 genomes]
rs7301125	0.86[EUR][1000 genomes]
rs7303202	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7304793	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7306387	0.81[EUR][1000 genomes]
rs7308872	0.83[ASN][1000 genomes]
rs7310507	0.81[EUR][1000 genomes]
rs7487150	0.93[ASN][1000 genomes]
rs7959129	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7964642	0.93[ASN][1000 genomes]
rs7969251	0.82[EUR][1000 genomes]
rs7979474	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs829125	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs939631	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs951591	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv976745	chr12:51203441-51215185	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51180800-51204400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:51188600-51207800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:51190200-51215200	Weak transcription	Pancreas	Pancrea
4	chr12:51193200-51204400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:51193200-51207600	Weak transcription	Fetal Heart	heart
6	chr12:51193200-51207800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:51193200-51207800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:51193200-51207800	Weak transcription	Esophagus	oesophagus
9	chr12:51193200-51208000	Weak transcription	Small Intestine	intestine
10	chr12:51193200-51211200	Weak transcription	Aorta	Aorta
11	chr12:51193400-51207800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:51193800-51204200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:51193800-51204400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr12:51193800-51204400	Weak transcription	Fetal Brain Male	brain
15	chr12:51194000-51204200	Weak transcription	NHLF	lung
16	chr12:51194000-51204400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr12:51194000-51204400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:51194000-51204400	Weak transcription	NHEK	skin
19	chr12:51194000-51204600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:51194400-51204400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:51194400-51204400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:51194400-51204400	Weak transcription	Right Ventricle	heart
23	chr12:51194400-51204400	Weak transcription	HSMMtube	muscle
24	chr12:51194400-51204400	Weak transcription	NH-A	brain
25	chr12:51194400-51204400	Weak transcription	NHDF-Ad	bronchial
26	chr12:51194400-51204600	Weak transcription	Brain Angular Gyrus	brain
27	chr12:51194400-51204600	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:51194400-51207800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:51194600-51204200	Weak transcription	HMEC	breast
30	chr12:51194600-51204400	Weak transcription	Brain Germinal Matrix	brain
31	chr12:51194600-51204400	Weak transcription	Ovary	ovary
32	chr12:51194600-51207800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr12:51194600-51214600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:51194800-51204400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:51194800-51209200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr12:51195600-51204400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:51195600-51204400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:51195600-51204400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:51195600-51204400	Weak transcription	Fetal Kidney	kidney
40	chr12:51195800-51204200	Weak transcription	GM12878-XiMat	blood
41	chr12:51198600-51215400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:51199600-51209400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:51200400-51204200	Weak transcription	Spleen	Spleen
44	chr12:51200400-51209200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:51200600-51222200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:51201000-51204400	Weak transcription	Fetal Brain Female	brain
47	chr12:51201400-51206600	Strong transcription	Dnd41	blood
48	chr12:51201400-51213800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:51201600-51204400	Weak transcription	Primary T cells from cord blood	blood
50	chr12:51201600-51212400	Strong transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links