Variant report

Variant	rs2054865
Chromosome Location	chr11:67951014-67951015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr11:67950626-67951093	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:67950651..67952322-chr11:67979433..67982221,2	MCF-7	breast:
2	chr11:67936765..67939586-chr11:67949122..67951263,2	MCF-7	breast:

Variant related genes	Relation type
SUV420H1	TF binding region
ENSG00000110066	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10896298	0.87[ASN][1000 genomes]
rs10896301	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896303	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896304	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10896305	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12225316	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894204	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2011157	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34236202	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34493482	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4345973	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4930228	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4930229	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930230	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4930561	0.87[ASN][1000 genomes]
rs4930563	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4930564	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61890513	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7950452	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv825963	chr11:67763676-68197054	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	149 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2054865	SUV420H1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67915000-67973800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:67922600-67956600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:67924400-67956600	Strong transcription	Fetal Intestine Large	intestine
4	chr11:67924400-67956800	Strong transcription	Primary T cells from cord blood	blood
5	chr11:67924400-67957000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:67924600-67956400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr11:67924600-67956600	Strong transcription	Fetal Muscle Leg	muscle
8	chr11:67925200-67955000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr11:67928000-67956600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr11:67928600-67955400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:67928800-67954200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:67928800-67954600	Strong transcription	Dnd41	blood
13	chr11:67928800-67955200	Strong transcription	Primary B cells from peripheral blood	blood
14	chr11:67929000-67954400	Strong transcription	Adipose Nuclei	Adipose
15	chr11:67929000-67955200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr11:67929000-67957600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:67929200-67956800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:67929200-67957600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:67929400-67953400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr11:67929600-67954800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr11:67930000-67954000	Strong transcription	Placenta	Placenta
22	chr11:67930000-67955400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:67930400-67953200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr11:67930400-67954200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:67931200-67954800	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr11:67931400-67957600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:67932400-67954400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:67932400-67956800	Strong transcription	Fetal Thymus	thymus
29	chr11:67932800-67954200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr11:67934400-67955600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr11:67938200-67953800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr11:67938200-67961200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:67938600-67960600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:67939200-67953200	Weak transcription	Small Intestine	intestine
35	chr11:67940200-67951400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:67940400-67955600	Weak transcription	NHLF	lung
37	chr11:67941800-67958200	Weak transcription	Esophagus	oesophagus
38	chr11:67942000-67951200	Weak transcription	HMEC	breast
39	chr11:67942000-67953000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr11:67942200-67951400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:67942200-67953200	Strong transcription	Liver	Liver
42	chr11:67942200-67954800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr11:67942200-67959600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr11:67942400-67953600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr11:67942600-67952200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr11:67942800-67951400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr11:67942800-67953200	Weak transcription	NHEK	skin
48	chr11:67942800-67953800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr11:67942800-67959200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:67943400-67960200	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links