Variant report

Variant	rs658657
Chromosome Location	chr21:46184864-46184865
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:46179049..46181876-chr21:46183341..46186313,2	K562	blood:
2	chr21:46183507..46185019-chr21:46346886..46349723,2	MCF-7	breast:
3	chr21:46179049..46181876-chr21:46183341..46186313,3	K562	blood:
4	chr21:46184069..46185902-chr21:46205323..46207249,2	MCF-7	breast:
5	chr21:46182776..46184894-chr21:46189262..46192289,3	K562	blood:
6	chr21:46184586..46187452-chr21:46187793..46189728,3	MCF-7	breast:
7	chr21:46181841..46189587-chr21:46189919..46197097,16	MCF-7	breast:
8	chr21:46168183..46170005-chr21:46182866..46185024,2	MCF-7	breast:
9	chr21:46171917..46177806-chr21:46181342..46188371,13	MCF-7	breast:
10	chr21:46124017..46124542-chr21:46184417..46184993,2	MCF-7	breast:
11	chr21:46182055..46185052-chr21:46201680..46204266,2	MCF-7	breast:
12	chr21:46184622..46186979-chr21:46203808..46205316,2	MCF-7	breast:
13	chr21:46171125..46175584-chr21:46182573..46186541,7	MCF-7	breast:
14	chr21:46181840..46185418-chr21:46198665..46202269,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160255	Chromatin interaction
ENSG00000184787	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1060564	0.90[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11569	0.90[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13048108	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13049333	0.90[CEU][hapmap];0.93[JPT][hapmap]
rs180317	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs183518	0.90[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs184633	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2329902	0.85[CEU][hapmap];0.85[JPT][hapmap];0.82[YRI][hapmap];0.85[AMR][1000 genomes]
rs235267	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235268	0.87[AMR][1000 genomes]
rs235269	0.85[ASN][1000 genomes]
rs235270	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs235271	0.89[CEU][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235272	0.90[CEU][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235275	0.90[CEU][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235337	0.90[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs235352	0.90[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235353	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235358	0.90[CEU][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs235360	0.90[CEU][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs235361	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs235369	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838695	0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3788134	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs434608	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs657730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs658637	0.88[ASN][1000 genomes]
rs660385	0.87[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs690626	0.90[CEU][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs7280306	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs84188	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][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	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	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs658657	UBE2G2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46168000-46185800	Weak transcription	Right Atrium	heart
2	chr21:46181200-46188000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr21:46181600-46185000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr21:46181800-46185000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr21:46181800-46185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:46181800-46188000	Weak transcription	Fetal Intestine Small	intestine
7	chr21:46181800-46188400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr21:46182000-46186400	Weak transcription	Fetal Muscle Leg	muscle
9	chr21:46182200-46185000	Weak transcription	Fetal Intestine Large	intestine
10	chr21:46182200-46189000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr21:46182400-46187000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr21:46182600-46188600	Weak transcription	Liver	Liver
13	chr21:46183400-46185600	Weak transcription	Fetal Lung	lung
14	chr21:46183600-46190800	Weak transcription	A549	lung
15	chr21:46183800-46185000	Weak transcription	Gastric	stomach
16	chr21:46183800-46185000	Weak transcription	Pancreas	Pancrea
17	chr21:46183800-46186800	Enhancers	Esophagus	oesophagus
18	chr21:46184200-46185200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr21:46184400-46185000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr21:46184400-46185200	Flanking Active TSS	HepG2	liver
21	chr21:46184400-46186000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr21:46184400-46187200	Enhancers	Primary T cells fromperipheralblood	blood
23	chr21:46184400-46187400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr21:46184600-46185000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr21:46184600-46185000	Bivalent Enhancer	NHEK	skin
26	chr21:46184600-46185200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:46184600-46185400	Enhancers	K562	blood
28	chr21:46184600-46185800	Enhancers	Stomach Mucosa	stomach
29	chr21:46184600-46186000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr21:46184600-46186000	Genic enhancers	Spleen	Spleen
31	chr21:46184600-46186200	Enhancers	Right Ventricle	heart
32	chr21:46184600-46186400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr21:46184600-46186400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr21:46184600-46186400	Enhancers	HSMM	muscle
35	chr21:46184600-46186600	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr21:46184600-46186600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr21:46184600-46186800	Enhancers	Placenta	Placenta
38	chr21:46184600-46186800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr21:46184600-46187200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr21:46184600-46187600	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr21:46184600-46189000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr21:46184600-46189200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr21:46184800-46185000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr21:46184800-46185000	Bivalent Enhancer	Adipose Nuclei	Adipose
45	chr21:46184800-46185000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
46	chr21:46184800-46185000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr21:46184800-46185600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr21:46184800-46185600	Enhancers	Duodenum Mucosa	Duodenum
49	chr21:46184800-46186000	Enhancers	Muscle Satellite Cultured Cells	--
50	chr21:46184800-46186000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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