Variant report

Variant	rs26654
Chromosome Location	chr5:96140367-96140368
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	chr5:96140146..96144558-chr5:96269495..96273172,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247121	Chromatin interaction
ENSG00000113441	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs149189	0.89[ASN][1000 genomes]
rs149431	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149482	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs149544	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs151823	0.82[CHB][hapmap]
rs151908	0.94[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs151909	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs151910	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs151911	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs151940	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs151953	0.87[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs151954	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs151964	0.89[ASN][1000 genomes]
rs152468	0.82[CHB][hapmap]
rs184971	0.81[CHB][hapmap]
rs193482	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs246453	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs246454	0.86[ASN][1000 genomes]
rs246455	0.86[ASN][1000 genomes]
rs2549805	0.82[CHB][hapmap]
rs26489	0.89[ASN][1000 genomes]
rs26490	0.86[ASN][1000 genomes]
rs26491	0.90[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs26493	0.82[CHB][hapmap]
rs26495	0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs26496	0.90[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs26497	0.89[ASN][1000 genomes]
rs26498	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs26500	0.89[ASN][1000 genomes]
rs26510	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs26512	0.87[ASN][1000 genomes]
rs26653	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27043	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs27044	0.82[CHB][hapmap]
rs27045	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs27432	0.82[CHB][hapmap]
rs27434	0.91[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs27529	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs27640	0.89[ASN][1000 genomes]
rs27694	0.82[CHB][hapmap]
rs27710	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs28119	0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs28129	0.95[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28333	0.89[ASN][1000 genomes]
rs28337	0.89[ASN][1000 genomes]
rs30185	0.89[ASN][1000 genomes]
rs30186	0.91[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs30187	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs30376	0.86[CHB][hapmap]
rs30378	0.90[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs30379	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs30380	0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs34735	0.82[CHB][hapmap]
rs34750	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34751	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34752	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34753	0.95[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34755	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs34756	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34757	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34759	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34760	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34761	0.92[EUR][1000 genomes]
rs34762	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34764	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35134	0.95[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40090	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs40091	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs40604	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs42398	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs42443	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs467735	0.86[ASN][1000 genomes]
rs468130	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs469674	0.87[ASN][1000 genomes]
rs469758	0.91[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs469783	0.86[CHB][hapmap];0.89[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs695965	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs845028	0.82[CHB][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs26654	ERAP2	cis	lymphoblastoid	seeQTL
rs26654	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs26654	ERAP1	cis	Whole Blood	GTEx
rs26654	ERAP1	cis	lung	GTEx

Chromatin state (count:122 , 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	chr5:96127400-96142600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:96127400-96142600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr5:96127400-96142600	Weak transcription	NH-A	brain
12	chr5:96127600-96141600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:96127600-96142800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:96132200-96141400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:96132200-96142800	Weak transcription	HSMM	muscle
16	chr5:96132600-96142000	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:96132600-96142600	Weak transcription	Fetal Brain Female	brain
18	chr5:96132800-96141800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:96132800-96142600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:96133000-96141200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:96133000-96141200	Weak transcription	K562	blood
22	chr5:96133000-96141400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr5:96133000-96141400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr5:96133000-96142000	Weak transcription	Hela-S3	cervix
25	chr5:96133000-96142200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:96133000-96142200	Weak transcription	Fetal Kidney	kidney
27	chr5:96133000-96142600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:96133000-96142600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:96133000-96142800	Weak transcription	Fetal Brain Male	brain
30	chr5:96133000-96142800	Weak transcription	HSMMtube	muscle
31	chr5:96133200-96141200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:96133200-96141200	Weak transcription	HepG2	liver
33	chr5:96133200-96142000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:96133200-96142000	Weak transcription	NHDF-Ad	bronchial
35	chr5:96133200-96142600	Weak transcription	HUVEC	blood vessel
36	chr5:96133200-96142800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:96133800-96142800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:96135000-96141200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr5:96135800-96141600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:96135800-96141800	Weak transcription	Brain Angular Gyrus	brain
41	chr5:96136000-96141200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr5:96136000-96142600	Weak transcription	Fetal Heart	heart
43	chr5:96136400-96141400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:96136800-96141200	Weak transcription	HMEC	breast
45	chr5:96136800-96141800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr5:96136800-96142000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:96137000-96140600	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr5:96137000-96141200	Weak transcription	Colonic Mucosa	Colon
49	chr5:96137000-96141200	Weak transcription	Colon Smooth Muscle	Colon
50	chr5:96137000-96141200	Weak transcription	Fetal Lung	lung

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