Variant report

Variant	rs407133
Chromosome Location	chr21:46571889-46571890
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46492313..46496810-chr21:46570892..46575986,6	K562	blood:
2	chr21:46571237..46574001-chr21:46707814..46709367,2	K562	blood:
3	chr21:46570712..46573836-chr21:46580844..46582723,4	K562	blood:
4	chr21:46571468..46573324-chr21:46581267..46583442,2	MCF-7	breast:
5	chr21:46564488..46569324-chr21:46569592..46573280,6	K562	blood:
6	chr2:60006171..60008805-chr21:46571056..46573707,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235374	Chromatin interaction
ENSG00000215447	Chromatin interaction
ENSG00000197381	Chromatin interaction
ENSG00000268856	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11088982	0.83[CEU][hapmap]
rs11088983	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs12185823	0.81[CEU][hapmap]
rs13047803	0.85[CEU][hapmap]
rs1537122	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1537123	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1556317	0.80[CEU][hapmap]
rs2225434	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2246081	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2838797	0.84[CEU][hapmap]
rs2838799	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap]
rs2838800	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2838803	0.81[CEU][hapmap]
rs2838806	0.88[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2838807	0.85[CEU][hapmap]
rs2838813	0.88[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2838815	0.88[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2849618	0.80[ASN][1000 genomes]
rs367986	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap]
rs372519	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs373037	0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs377902	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3788183	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs394608	0.94[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.83[ASN][1000 genomes]
rs394872	0.83[ASN][1000 genomes]
rs395761	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[ASN][1000 genomes]
rs397092	0.88[CEU][hapmap];0.83[ASN][1000 genomes]
rs400997	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs403694	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs412646	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs421716	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs427943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4818766	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4819030	0.85[CEU][hapmap]
rs4819031	0.83[CEU][hapmap]
rs7281416	0.81[CEU][hapmap]
rs8128889	0.81[CEU][hapmap]
rs8130224	0.81[CEU][hapmap]
rs8134789	0.85[CEU][hapmap]
rs983749	0.81[CEU][hapmap]
rs984791	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]

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	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46553400-46574600	Weak transcription	Fetal Heart	heart
2	chr21:46555200-46574600	Weak transcription	Right Atrium	heart
3	chr21:46556600-46581000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr21:46557000-46604800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:46557200-46591800	Weak transcription	HUVEC	blood vessel
6	chr21:46557400-46577800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr21:46557600-46573400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr21:46557600-46582600	Weak transcription	Psoas Muscle	Psoas
9	chr21:46558600-46588800	Weak transcription	Colonic Mucosa	Colon
10	chr21:46560800-46578600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr21:46560800-46586400	Weak transcription	Liver	Liver
12	chr21:46561400-46576000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr21:46562800-46572600	Weak transcription	Brain Anterior Caudate	brain
14	chr21:46563000-46595600	Weak transcription	Pancreas	Pancrea
15	chr21:46563200-46576600	Weak transcription	Brain Hippocampus Middle	brain
16	chr21:46566000-46573200	Weak transcription	Osteobl	bone
17	chr21:46566000-46583200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr21:46567200-46573200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr21:46568200-46572000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr21:46568200-46572200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr21:46568400-46573600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr21:46568400-46581400	Weak transcription	Gastric	stomach
23	chr21:46569000-46574000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr21:46569000-46587000	Weak transcription	NHEK	skin
25	chr21:46569200-46573400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr21:46570400-46572600	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr21:46570400-46582600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr21:46570600-46572400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr21:46570600-46572400	Enhancers	K562	blood
30	chr21:46570600-46573800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr21:46570600-46575400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr21:46570600-46575400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr21:46570800-46572000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr21:46570800-46572000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr21:46570800-46572000	Enhancers	Fetal Lung	lung
36	chr21:46570800-46572000	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr21:46570800-46575400	Enhancers	Fetal Muscle Leg	muscle
38	chr21:46571000-46572000	Enhancers	Primary T cells from cord blood	blood
39	chr21:46571000-46572200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr21:46571000-46572400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr21:46571000-46572400	Enhancers	Fetal Brain Female	brain
42	chr21:46571000-46572400	Enhancers	Fetal Thymus	thymus
43	chr21:46571000-46574000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr21:46571000-46580000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr21:46571200-46572000	Enhancers	Primary B cells from cord blood	blood
46	chr21:46571200-46572200	Enhancers	Primary hematopoietic stem cells	blood
47	chr21:46571200-46572200	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr21:46571200-46572200	Enhancers	Brain Germinal Matrix	brain
49	chr21:46571400-46572000	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr21:46571400-46572000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links