Variant report

Variant	rs12278859
Chromosome Location	chr11:59421699-59421700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:59381971..59384335-chr11:59420377..59423373,2	K562	blood:
2	chr11:59420045..59421714-chr11:59422885..59424724,2	K562	blood:
3	chr11:59420557..59422154-chr11:59434243..59436764,2	MCF-7	breast:
4	chr11:59409381..59412375-chr11:59418263..59422142,3	K562	blood:

Variant related genes	Relation type
ENSG00000166889	Chromatin interaction
ENSG00000255139	Chromatin interaction
ENSG00000110048	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs1121991	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11230020	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11230027	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11230037	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151063	0.88[EUR][1000 genomes]
rs1151064	0.88[EUR][1000 genomes]
rs11821333	0.92[EUR][1000 genomes]
rs11821465	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12271188	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12272588	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12276505	0.83[ASN][1000 genomes]
rs12278910	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12280606	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12281969	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12285828	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12287975	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12289162	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12289921	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12292682	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12797334	0.92[EUR][1000 genomes]
rs1287111	0.88[EUR][1000 genomes]
rs1287441	0.92[EUR][1000 genomes]
rs1287442	0.90[EUR][1000 genomes]
rs1287446	0.92[EUR][1000 genomes]
rs1287448	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1287449	0.83[ASN][1000 genomes]
rs1290457	0.92[EUR][1000 genomes]
rs1290459	0.92[EUR][1000 genomes]
rs1290466	0.81[EUR][1000 genomes]
rs1299800	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17046	0.92[EUR][1000 genomes]
rs17153910	0.92[EUR][1000 genomes]
rs17154029	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17154134	0.88[EUR][1000 genomes]
rs17154138	0.88[EUR][1000 genomes]
rs17154146	0.88[EUR][1000 genomes]
rs17154149	0.88[EUR][1000 genomes]
rs17154157	0.88[EUR][1000 genomes]
rs17154165	0.88[EUR][1000 genomes]
rs17154169	0.88[EUR][1000 genomes]
rs17154175	0.88[EUR][1000 genomes]
rs17154180	0.88[EUR][1000 genomes]
rs17154195	0.88[EUR][1000 genomes]
rs17154200	0.88[EUR][1000 genomes]
rs17154222	0.88[EUR][1000 genomes]
rs17154227	0.86[EUR][1000 genomes]
rs1783212	0.92[EUR][1000 genomes]
rs1938690	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186597	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2509274	0.88[EUR][1000 genomes]
rs2509275	0.86[EUR][1000 genomes]
rs2509276	0.88[EUR][1000 genomes]
rs2509290	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2509730	0.88[EUR][1000 genomes]
rs2927183	0.92[EUR][1000 genomes]
rs2957223	0.84[EUR][1000 genomes]
rs3015969	0.92[EUR][1000 genomes]
rs3019740	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3110322	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3132748	0.92[EUR][1000 genomes]
rs34350918	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781792	0.88[EUR][1000 genomes]
rs3781793	0.88[EUR][1000 genomes]
rs3862660	0.88[EUR][1000 genomes]
rs41384548	0.88[EUR][1000 genomes]
rs4301803	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356243	0.86[EUR][1000 genomes]
rs4393334	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4515985	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs472177	0.92[EUR][1000 genomes]
rs473087	0.92[EUR][1000 genomes]
rs473490	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs474844	0.92[EUR][1000 genomes]
rs475706	0.92[EUR][1000 genomes]
rs478167	0.88[EUR][1000 genomes]
rs482355	0.88[EUR][1000 genomes]
rs482356	0.88[EUR][1000 genomes]
rs484895	0.88[EUR][1000 genomes]
rs485008	0.88[EUR][1000 genomes]
rs486587	0.88[EUR][1000 genomes]
rs488331	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs492652	0.92[EUR][1000 genomes]
rs4939294	0.92[EUR][1000 genomes]
rs495564	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs498388	0.92[EUR][1000 genomes]
rs504016	0.88[EUR][1000 genomes]
rs507235	0.88[EUR][1000 genomes]
rs510122	0.88[EUR][1000 genomes]
rs510249	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs511785	0.88[EUR][1000 genomes]
rs511957	0.92[EUR][1000 genomes]
rs512194	0.80[EUR][1000 genomes]
rs512695	0.88[EUR][1000 genomes]
rs516912	0.88[EUR][1000 genomes]
rs519605	0.88[EUR][1000 genomes]
rs519865	0.92[EUR][1000 genomes]
rs519873	0.92[EUR][1000 genomes]
rs521330	0.88[EUR][1000 genomes]
rs523016	0.88[EUR][1000 genomes]
rs528525	0.88[EUR][1000 genomes]
rs529270	0.88[EUR][1000 genomes]
rs532838	0.92[EUR][1000 genomes]
rs536910	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs537625	0.92[EUR][1000 genomes]
rs540684	0.92[EUR][1000 genomes]
rs550189	0.92[EUR][1000 genomes]
rs550822	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs552601	0.92[EUR][1000 genomes]
rs553700	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs554149	0.92[EUR][1000 genomes]
rs554848	0.88[EUR][1000 genomes]
rs555175	0.88[EUR][1000 genomes]
rs55667192	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs561604	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs563276	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs565983	0.88[EUR][1000 genomes]
rs567485	0.88[EUR][1000 genomes]
rs567603	0.88[EUR][1000 genomes]
rs567994	0.90[EUR][1000 genomes]
rs569326	0.88[EUR][1000 genomes]
rs573592	0.88[EUR][1000 genomes]
rs57529518	0.88[EUR][1000 genomes]
rs57871852	0.88[EUR][1000 genomes]
rs579192	0.92[EUR][1000 genomes]
rs579373	0.88[EUR][1000 genomes]
rs580242	0.92[EUR][1000 genomes]
rs58169611	0.88[EUR][1000 genomes]
rs58775794	0.88[EUR][1000 genomes]
rs60009036	0.88[EUR][1000 genomes]
rs60094706	0.88[EUR][1000 genomes]
rs61636608	0.88[EUR][1000 genomes]
rs6591540	0.81[EUR][1000 genomes]
rs6591541	0.92[EUR][1000 genomes]
rs693110	0.92[EUR][1000 genomes]
rs7108731	0.81[EUR][1000 genomes]
rs7114773	0.88[EUR][1000 genomes]
rs7116567	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7119778	0.88[EUR][1000 genomes]
rs7123969	0.86[EUR][1000 genomes]
rs7124813	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7126593	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131059	0.88[EUR][1000 genomes]
rs73486934	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73486962	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73486971	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73486979	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73486988	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73486997	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73488804	0.86[AMR][1000 genomes]
rs7933970	0.86[EUR][1000 genomes]
rs7941643	0.92[EUR][1000 genomes]
rs7946152	0.88[EUR][1000 genomes]
rs7947036	0.88[EUR][1000 genomes]
rs7947514	0.88[EUR][1000 genomes]
rs7952024	0.88[EUR][1000 genomes]
rs7952367	0.92[EUR][1000 genomes]
rs8280	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1797571	chr11:59383323-59424688	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv1797737	chr11:59383323-59424688	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv1802782	chr11:59383323-59448068	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv832172	chr11:59396407-59431115	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59395600-59434600	Weak transcription	Stomach Mucosa	stomach
2	chr11:59402200-59427000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:59402200-59432400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr11:59402200-59434000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr11:59402400-59427800	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr11:59402400-59428200	Strong transcription	Primary T cells from cord blood	blood
7	chr11:59402600-59424200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:59402600-59426800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr11:59402600-59427200	Strong transcription	Primary hematopoietic stem cells	blood
10	chr11:59402600-59427400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:59402600-59427600	Strong transcription	Adipose Nuclei	Adipose
12	chr11:59402600-59427600	Strong transcription	GM12878-XiMat	blood
13	chr11:59402600-59428000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:59402600-59428000	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr11:59402600-59428400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr11:59402600-59428400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr11:59402600-59428600	Strong transcription	Fetal Muscle Leg	muscle
18	chr11:59402600-59429000	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:59402600-59434000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:59402600-59434000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:59402600-59434200	Strong transcription	Fetal Muscle Trunk	muscle
22	chr11:59402600-59434400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr11:59402800-59426600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:59402800-59427000	Strong transcription	Ovary	ovary
25	chr11:59402800-59427200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr11:59402800-59427200	Strong transcription	HUVEC	blood vessel
27	chr11:59402800-59428000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr11:59402800-59428000	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr11:59402800-59428000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:59402800-59428000	Strong transcription	Placenta	Placenta
31	chr11:59402800-59428400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr11:59402800-59428600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr11:59402800-59428800	Strong transcription	Thymus	Thymus
34	chr11:59402800-59429800	Strong transcription	Dnd41	blood
35	chr11:59402800-59431600	Strong transcription	Fetal Intestine Large	intestine
36	chr11:59402800-59434200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr11:59402800-59434200	Strong transcription	Fetal Thymus	thymus
38	chr11:59402800-59434400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:59403000-59426600	Strong transcription	Brain Hippocampus Middle	brain
40	chr11:59403000-59427000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr11:59403000-59427200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr11:59403000-59429200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:59403200-59429000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:59403200-59434600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:59403400-59427600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:59403400-59430000	Strong transcription	Osteobl	bone
47	chr11:59403400-59434400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr11:59403400-59434400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:59403600-59434600	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr11:59403800-59429600	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links