Variant report

Variant	rs17045296
Chromosome Location	chr2:54053241-54053242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:62609118..62609651-chr2:54053034..54053551,3	Hela-S3	cervix:
2	chr10:103124609..103125127-chr2:54053027..54053548,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction
ENSG00000222414	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10204047	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10204432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10490472	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10490473	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13387421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13404007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13426962	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17039534	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17045109	0.80[EUR][1000 genomes]
rs17045123	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17045139	1.00[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17045239	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17045241	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17045262	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17045286	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2056650	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2287339	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2287342	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2287346	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2287347	0.89[ASN][1000 genomes]
rs2302876	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2302880	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28834518	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3213768	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3213774	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3755113	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755114	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3755115	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3755116	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3755119	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3770390	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770391	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3770396	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3815650	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3821079	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59951261	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60972886	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6545368	0.89[ASN][1000 genomes]
rs6724214	0.87[ASN][1000 genomes]
rs6761242	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72799242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72799275	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72901302	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72902916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72902923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72902926	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72902929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72902937	0.80[EUR][1000 genomes]
rs7601553	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7605552	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54015200-54053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:54015600-54054600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:54015800-54054000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:54023000-54053800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:54025800-54062000	Weak transcription	Right Ventricle	heart
6	chr2:54025800-54085600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:54030400-54063000	Weak transcription	Esophagus	oesophagus
8	chr2:54040200-54055000	Weak transcription	Fetal Heart	heart
9	chr2:54041400-54054600	Weak transcription	Psoas Muscle	Psoas
10	chr2:54041400-54056400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:54042800-54062200	Weak transcription	Fetal Kidney	kidney
12	chr2:54043000-54053800	Weak transcription	NHEK	skin
13	chr2:54043200-54053800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:54043400-54053600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:54046000-54053600	Weak transcription	NH-A	brain
16	chr2:54046600-54080200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr2:54046600-54080200	Weak transcription	NHDF-Ad	bronchial
18	chr2:54046800-54054000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:54046800-54054200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:54046800-54054200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:54046800-54056800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:54046800-54060400	Weak transcription	Primary B cells from cord blood	blood
23	chr2:54046800-54070800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:54046800-54080400	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:54047000-54053800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:54047000-54054000	Weak transcription	NHLF	lung
27	chr2:54047000-54056600	Weak transcription	Brain Germinal Matrix	brain
28	chr2:54047000-54060600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr2:54047000-54061400	Weak transcription	Fetal Thymus	thymus
30	chr2:54047000-54080200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:54047000-54080200	Weak transcription	A549	lung
32	chr2:54047000-54080400	Weak transcription	Gastric	stomach
33	chr2:54047000-54080400	Weak transcription	Pancreas	Pancrea
34	chr2:54047000-54080800	Weak transcription	Aorta	Aorta
35	chr2:54047200-54053800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:54047200-54053800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:54047200-54054000	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:54047200-54054200	Weak transcription	Left Ventricle	heart
39	chr2:54047200-54054600	Weak transcription	Lung	lung
40	chr2:54047200-54055200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:54047200-54056800	Weak transcription	HSMMtube	muscle
42	chr2:54047200-54059600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr2:54047200-54061800	Weak transcription	Thymus	Thymus
44	chr2:54047200-54063000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:54047200-54067600	Weak transcription	HSMM	muscle
46	chr2:54047200-54070800	Weak transcription	Placenta	Placenta
47	chr2:54047200-54077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:54047200-54080000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:54047200-54080200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:54047200-54080200	Weak transcription	Muscle Satellite Cultured Cells	--

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