Variant report

Variant	rs55695458
Chromosome Location	chr5:96048943-96048944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96044782..96047336-chr5:96048549..96051619,3	K562	blood:
2	chr5:96045462..96047698-chr5:96048797..96050633,2	MCF-7	breast:
3	chr5:96042717..96044579-chr5:96047527..96049294,2	K562	blood:
4	chr5:96037628..96039907-chr5:96046806..96049372,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10447215	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10515244	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11738135	1.00[EUR][1000 genomes]
rs11739280	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11744642	0.89[AMR][1000 genomes]
rs11745122	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11750399	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11750400	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11750510	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12188168	0.99[EUR][1000 genomes]
rs1559085	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17082200	1.00[EUR][1000 genomes]
rs17086588	0.99[EUR][1000 genomes]
rs17400685	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17400741	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17479052	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34942552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56116814	0.99[EUR][1000 genomes]
rs56122780	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56257788	1.00[EUR][1000 genomes]
rs6864233	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72772090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72772091	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72772092	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72772095	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72773919	1.00[AFR][1000 genomes]

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	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96039200-96050600	Weak transcription	Gastric	stomach
2	chr5:96039200-96054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:96039200-96054400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:96039200-96054400	Weak transcription	Spleen	Spleen
5	chr5:96039200-96059800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:96039400-96050200	Weak transcription	Aorta	Aorta
7	chr5:96039600-96063600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:96039800-96049600	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:96039800-96049800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:96040000-96049600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:96040000-96049800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:96040000-96050000	Weak transcription	Primary T cells from cord blood	blood
13	chr5:96040000-96050000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr5:96040000-96050200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:96040000-96050400	Weak transcription	Primary B cells from cord blood	blood
16	chr5:96040000-96054400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:96040000-96054400	Weak transcription	Fetal Stomach	stomach
18	chr5:96040200-96049400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:96040200-96049800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:96040200-96050200	Weak transcription	Brain Substantia Nigra	brain
21	chr5:96040200-96050600	Weak transcription	Brain Anterior Caudate	brain
22	chr5:96040400-96049800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:96040600-96050200	Weak transcription	Fetal Kidney	kidney
24	chr5:96041600-96054600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr5:96041800-96049600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr5:96042800-96076200	Weak transcription	GM12878-XiMat	blood
27	chr5:96043600-96054400	Weak transcription	Esophagus	oesophagus
28	chr5:96044400-96049600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:96044800-96050200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr5:96045000-96049200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:96045000-96049600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr5:96045000-96049800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:96045000-96050200	Weak transcription	HUVEC	blood vessel
34	chr5:96045000-96052200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr5:96045200-96049800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:96045400-96050000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr5:96045400-96050000	Weak transcription	Hela-S3	cervix
38	chr5:96045600-96050000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:96045600-96050000	Weak transcription	HSMMtube	muscle
40	chr5:96045600-96050600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr5:96045800-96049600	Weak transcription	NHDF-Ad	bronchial
42	chr5:96045800-96049800	Weak transcription	NHLF	lung
43	chr5:96045800-96050000	Weak transcription	HSMM	muscle
44	chr5:96045800-96050000	Weak transcription	Osteobl	bone
45	chr5:96045800-96050400	Weak transcription	NH-A	brain
46	chr5:96045800-96056800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr5:96046000-96049800	Weak transcription	K562	blood
48	chr5:96046200-96050000	Weak transcription	HMEC	breast
49	chr5:96046400-96049600	Weak transcription	Psoas Muscle	Psoas
50	chr5:96046600-96050200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links