Variant report

Variant	rs10838533
Chromosome Location	chr11:45951306-45951307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45949947..45952714-chr11:45954303..45955932,2	MCF-7	breast:
2	chr11:45942146..45943725-chr11:45949877..45951840,2	K562	blood:
3	chr11:45950793..45953982-chr11:45956779..45958840,3	MCF-7	breast:
4	chr11:45867884..45870625-chr11:45950267..45953158,3	MCF-7	breast:
5	chr11:45949887..45952560-chr11:46020571..46022730,2	K562	blood:

Variant related genes	Relation type
ENSG00000121671	Chromatin interaction
ENSG00000165905	Chromatin interaction
ENSG00000135365	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10769176	0.80[CEU][hapmap]
rs10838535	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11038720	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11038742	0.81[CEU][hapmap]
rs11038745	0.83[AMR][1000 genomes]
rs1125290	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2945997	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2945999	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2946001	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2946003	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2946004	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2959087	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2959090	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2959091	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2959098	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2959099	0.91[CEU][hapmap];0.83[AMR][1000 genomes]
rs2959102	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4144718	0.95[CEU][hapmap];0.89[AMR][1000 genomes]
rs4237660	0.95[CEU][hapmap];0.89[AMR][1000 genomes]
rs6485654	0.85[CEU][hapmap]
rs7108028	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7108186	0.95[CEU][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7130281	0.85[AMR][1000 genomes]
rs7935308	0.89[AMR][1000 genomes]
rs7950336	0.95[CEU][hapmap];0.83[AMR][1000 genomes]
rs884668	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1047462	chr11:45898630-45953696	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv516442	chr11:45899962-45983385	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	esv1794798	chr11:45903280-45953636	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	esv1805505	chr11:45912324-45956109	Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10838533	PHF21A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45941200-45953400	Weak transcription	Dnd41	blood
2	chr11:45944800-45951800	Weak transcription	Aorta	Aorta
3	chr11:45944800-45955200	Weak transcription	Ovary	ovary
4	chr11:45945000-45953200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr11:45945200-45952600	Weak transcription	Brain Hippocampus Middle	brain
6	chr11:45945200-45953000	Weak transcription	Brain Anterior Caudate	brain
7	chr11:45945200-45953200	Weak transcription	Liver	Liver
8	chr11:45945200-45954400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:45945200-45955000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:45945200-45955200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:45945200-45969400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:45946000-45951400	Weak transcription	K562	blood
13	chr11:45946400-45953000	Weak transcription	Right Atrium	heart
14	chr11:45946600-45952200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:45946800-45952200	Weak transcription	Fetal Brain Female	brain
16	chr11:45947000-45951600	Weak transcription	Brain Germinal Matrix	brain
17	chr11:45947400-45953600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:45947600-45951400	Strong transcription	Fetal Intestine Small	intestine
19	chr11:45947600-45952000	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:45947600-45953000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:45947600-45953200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:45947800-45951400	Weak transcription	Thymus	Thymus
23	chr11:45947800-45951600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr11:45947800-45952600	Enhancers	Placenta	Placenta
25	chr11:45947800-45952800	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:45948200-45951400	Weak transcription	Lung	lung
27	chr11:45948200-45954800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:45948400-45951800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr11:45948600-45951400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr11:45948600-45953000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr11:45948800-45951400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr11:45948800-45957000	Weak transcription	NH-A	brain
33	chr11:45949000-45951400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:45949000-45953800	Weak transcription	Osteobl	bone
35	chr11:45949200-45951400	Weak transcription	Fetal Intestine Large	intestine
36	chr11:45949200-45951600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr11:45949200-45953400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:45949200-45954800	Strong transcription	Fetal Stomach	stomach
39	chr11:45949200-45956400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr11:45949400-45957000	Enhancers	HMEC	breast
41	chr11:45949600-45953400	Weak transcription	Adipose Nuclei	Adipose
42	chr11:45949600-45956600	Weak transcription	NHDF-Ad	bronchial
43	chr11:45949800-45956800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:45950000-45951800	Enhancers	Esophagus	oesophagus
45	chr11:45950000-45951800	Enhancers	NHEK	skin
46	chr11:45950000-45952400	Weak transcription	NHLF	lung
47	chr11:45950000-45954600	Weak transcription	Brain Substantia Nigra	brain
48	chr11:45950200-45951400	Weak transcription	Fetal Thymus	thymus
49	chr11:45950200-45951800	Weak transcription	Spleen	Spleen
50	chr11:45950200-45953000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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