Variant report

Variant	rs40090
Chromosome Location	chr5:96154754-96154755
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96154679..96157683-chr5:96161689..96165620,3	K562	blood:
2	chr5:96142124..96146941-chr5:96154281..96159448,6	MCF-7	breast:
3	chr5:96153135..96156038-chr5:96157520..96159852,2	MCF-7	breast:
4	chr5:96153073..96155340-chr5:96156797..96159342,3	K562	blood:

Variant related genes	Relation type
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs149431	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs149482	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs149544	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151908	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151909	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151910	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151911	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151953	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151954	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs152280	0.84[ASN][1000 genomes]
rs152466	0.80[ASN][1000 genomes]
rs187387	0.80[ASN][1000 genomes]
rs190298	0.80[ASN][1000 genomes]
rs193482	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26653	0.83[ASN][1000 genomes]
rs26654	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26655	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs27527	0.84[ASN][1000 genomes]
rs27645	0.80[ASN][1000 genomes]
rs28129	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34737	0.80[ASN][1000 genomes]
rs34750	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34751	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34752	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34753	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34755	0.92[ASN][1000 genomes]
rs34756	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34757	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34759	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34760	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34761	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34762	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34764	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35134	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40091	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs42443	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs468130	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs695965	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs40090	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs40090	ERAP1	cis	Whole Blood	GTEx
rs40090	ERAP1	cis	lung	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96144600-96156600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:96150400-96159800	Weak transcription	Fetal Intestine Large	intestine
3	chr5:96152200-96156600	Weak transcription	NHEK	skin
4	chr5:96152200-96158600	Weak transcription	Spleen	Spleen
5	chr5:96152400-96156600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr5:96152400-96156600	Weak transcription	HMEC	breast
7	chr5:96152400-96157000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:96152600-96156800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:96152600-96156800	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr5:96152600-96156800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:96152600-96157000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:96152800-96156600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:96152800-96156800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:96153000-96155400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr5:96153000-96156600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:96153000-96156600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr5:96153000-96156600	Weak transcription	Adipose Nuclei	Adipose
18	chr5:96153000-96156600	Weak transcription	HSMM	muscle
19	chr5:96153000-96156800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:96153000-96157200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr5:96153000-96157200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr5:96153000-96159200	Weak transcription	Right Atrium	heart
23	chr5:96153200-96155200	Enhancers	Primary T cells fromperipheralblood	blood
24	chr5:96153200-96155800	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr5:96153200-96155800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr5:96153200-96159200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:96153600-96155800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr5:96153600-96156000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr5:96153600-96156600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr5:96153600-96156600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr5:96153600-96156800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr5:96153600-96157000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr5:96153600-96158800	Weak transcription	Fetal Intestine Small	intestine
34	chr5:96153600-96159200	Weak transcription	Osteobl	bone
35	chr5:96153800-96156800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:96154000-96157200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:96154200-96155000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:96154200-96156800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr5:96154200-96156800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:96154200-96158800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:96154400-96156800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr5:96154400-96156800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:96154400-96156800	Weak transcription	Thymus	Thymus
44	chr5:96154400-96157200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr5:96154400-96159400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:96154400-96160400	Enhancers	Dnd41	blood
47	chr5:96154600-96155000	Weak transcription	Primary T cells from cord blood	blood
48	chr5:96154600-96155000	Weak transcription	Fetal Thymus	thymus

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