Variant report

Variant	rs11887863
Chromosome Location	chr2:9739429-9739430
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:9731942..9734354-chr2:9738501..9740007,2	K562	blood:
2	chr2:9737361..9739506-chr2:9769982..9772140,2	K562	blood:

Variant related genes	Relation type
ENSG00000134308	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10169269	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10210225	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10929590	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1111976	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674769	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11674777	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11890807	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11902264	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12692388	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13415136	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2357157	0.94[ASN][1000 genomes]
rs3791748	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3951115	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4669400	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62119427	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6432018	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6432019	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6432020	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6432023	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432024	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6432025	0.94[ASN][1000 genomes]
rs6706227	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734469	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745213	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556678	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7556757	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7558086	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7565646	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7569485	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7596929	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	nsv580915	chr2:9308148-9844178	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv214045	chr2:9734039-9742991	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9696800-9767600	Weak transcription	Gastric	stomach
2	chr2:9719200-9747800	Weak transcription	Lung	lung
3	chr2:9723800-9739800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:9726000-9739800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:9732400-9747600	Weak transcription	Placenta	Placenta
6	chr2:9734000-9748000	Weak transcription	Pancreas	Pancrea
7	chr2:9734600-9748000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:9735200-9748400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:9735400-9739800	Weak transcription	Brain Substantia Nigra	brain
10	chr2:9735400-9748000	Weak transcription	Aorta	Aorta
11	chr2:9735400-9748000	Weak transcription	Spleen	Spleen
12	chr2:9735600-9748400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:9735800-9747600	Weak transcription	Stomach Mucosa	stomach
14	chr2:9735800-9748200	Weak transcription	Ovary	ovary
15	chr2:9736200-9739800	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:9737000-9742600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:9737000-9747800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:9737000-9748000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:9737200-9740000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr2:9737200-9740400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:9737200-9740800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:9737200-9742400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:9737200-9747400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:9737200-9748000	Weak transcription	Small Intestine	intestine
25	chr2:9737400-9747600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:9737400-9747600	Weak transcription	Hela-S3	cervix
27	chr2:9737400-9747800	Weak transcription	Fetal Heart	heart
28	chr2:9737800-9742000	ZNF genes & repeats	Fetal Brain Female	brain
29	chr2:9738000-9741000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:9738000-9741000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
31	chr2:9738000-9742800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
32	chr2:9738200-9739600	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr2:9738200-9740400	ZNF genes & repeats	Fetal Lung	lung
34	chr2:9738200-9741000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:9738200-9741200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:9738200-9741200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
37	chr2:9738200-9741400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:9738200-9741600	ZNF genes & repeats	Fetal Intestine Large	intestine
39	chr2:9738200-9741800	Strong transcription	Fetal Thymus	thymus
40	chr2:9738200-9742800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:9738200-9742800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:9738200-9742800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
43	chr2:9738200-9742800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:9738200-9743400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:9738200-9744400	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr2:9738400-9739600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
47	chr2:9738400-9739600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr2:9738400-9739800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr2:9738400-9740000	ZNF genes & repeats	Osteobl	bone
50	chr2:9738400-9740600	ZNF genes & repeats	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links