Variant report

Variant	rs26497
Chromosome Location	chr5:96138767-96138768
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	chr5:96137984..96139800-chr5:96270455..96273278,2	MCF-7	breast:
2	chr5:96130627..96133603-chr5:96137872..96139471,2	K562	blood:

Variant related genes	Relation type
ENSG00000113441	Chromatin interaction
ENSG00000247121	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs149189	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151823	0.82[ASN][1000 genomes]
rs151940	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs151964	0.99[ASN][1000 genomes]
rs152280	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs152466	0.82[ASN][1000 genomes]
rs152468	0.80[ASN][1000 genomes]
rs184971	0.80[ASN][1000 genomes]
rs187387	0.82[ASN][1000 genomes]
rs190298	0.82[ASN][1000 genomes]
rs245472	0.80[ASN][1000 genomes]
rs246453	0.97[ASN][1000 genomes]
rs246454	0.97[ASN][1000 genomes]
rs246455	0.97[ASN][1000 genomes]
rs2545629	0.80[ASN][1000 genomes]
rs26489	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26490	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26491	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26493	0.82[ASN][1000 genomes]
rs26495	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26496	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26498	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26500	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26510	0.99[ASN][1000 genomes]
rs26512	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26653	0.89[ASN][1000 genomes]
rs26654	0.89[ASN][1000 genomes]
rs26655	0.89[ASN][1000 genomes]
rs27043	0.82[ASN][1000 genomes]
rs27044	0.82[ASN][1000 genomes]
rs27045	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27432	0.84[ASN][1000 genomes]
rs27434	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27527	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27529	0.99[ASN][1000 genomes]
rs27640	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27645	0.82[ASN][1000 genomes]
rs27694	0.80[ASN][1000 genomes]
rs27710	0.99[ASN][1000 genomes]
rs28119	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28333	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28337	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30185	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30186	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30187	0.99[ASN][1000 genomes]
rs30334	0.88[ASN][1000 genomes]
rs30376	0.82[ASN][1000 genomes]
rs30378	0.97[ASN][1000 genomes]
rs30379	0.97[ASN][1000 genomes]
rs30380	0.97[ASN][1000 genomes]
rs34735	0.80[ASN][1000 genomes]
rs34737	0.82[ASN][1000 genomes]
rs34750	0.88[ASN][1000 genomes]
rs34751	0.88[ASN][1000 genomes]
rs34752	0.88[ASN][1000 genomes]
rs39840	0.82[ASN][1000 genomes]
rs39841	0.82[ASN][1000 genomes]
rs42398	0.82[ASN][1000 genomes]
rs467735	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs469367	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs469674	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs469758	0.97[ASN][1000 genomes]
rs469783	0.94[ASN][1000 genomes]
rs695965	0.89[ASN][1000 genomes]
rs845028	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv948703	chr5:96078309-96368839	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1027472	chr5:96081592-96337550	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1028741	chr5:96082401-96372165	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv949058	chr5:96082433-96390619	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv598963	chr5:96084776-96363407	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv432756	chr5:96113844-96234644	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv531967	chr5:96127842-96302702	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs26497	CTD-2260A17.1	cis	Whole Blood	GTEx
rs26497	ERAP1	cis	lung	GTEx
rs26497	ERAP1	cis	Whole Blood	GTEx
rs26497	ERAP1	cis	Nerve Tibial	GTEx
rs26497	ERAP1	cis	Esophagus Mucosa	GTEx
rs26497	ERAP1	cis	Skin Sun Exposed Lower leg	GTEx
rs26497	CTD-2260A17.3	cis	Whole Blood	GTEx
rs26497	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96115200-96141200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:96115400-96142000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:96116200-96141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:96119000-96142000	Weak transcription	A549	lung
5	chr5:96126800-96142800	Weak transcription	Brain Germinal Matrix	brain
6	chr5:96127000-96140400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:96127000-96142600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:96127000-96142800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:96127200-96139600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:96127200-96139800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr5:96127400-96142600	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr5:96127400-96142600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:96127400-96142600	Weak transcription	NH-A	brain
14	chr5:96127600-96141600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:96127600-96142800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:96132200-96141400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:96132200-96142800	Weak transcription	HSMM	muscle
18	chr5:96132600-96139000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:96132600-96142000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:96132600-96142600	Weak transcription	Fetal Brain Female	brain
21	chr5:96132800-96141800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:96132800-96142600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr5:96133000-96139200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:96133000-96139200	Weak transcription	NHLF	lung
25	chr5:96133000-96140200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:96133000-96141200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr5:96133000-96141200	Weak transcription	K562	blood
28	chr5:96133000-96141400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:96133000-96141400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:96133000-96142000	Weak transcription	Hela-S3	cervix
31	chr5:96133000-96142200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr5:96133000-96142200	Weak transcription	Fetal Kidney	kidney
33	chr5:96133000-96142600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:96133000-96142600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:96133000-96142800	Weak transcription	Fetal Brain Male	brain
36	chr5:96133000-96142800	Weak transcription	HSMMtube	muscle
37	chr5:96133200-96141200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:96133200-96141200	Weak transcription	HepG2	liver
39	chr5:96133200-96142000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:96133200-96142000	Weak transcription	NHDF-Ad	bronchial
41	chr5:96133200-96142600	Weak transcription	HUVEC	blood vessel
42	chr5:96133200-96142800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr5:96133800-96142800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr5:96135000-96141200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
45	chr5:96135600-96139600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr5:96135800-96141600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:96135800-96141800	Weak transcription	Brain Angular Gyrus	brain
48	chr5:96136000-96139200	Weak transcription	NHEK	skin
49	chr5:96136000-96141200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:96136000-96142600	Weak transcription	Fetal Heart	heart

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