Variant report

Variant	rs28129
Chromosome Location	chr5:96155518-96155519
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	chr5:96141844..96146815-chr5:96155332..96160391,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164307	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs149431	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149482	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs149544	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151909	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151953	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151954	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152280	0.87[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap];0.88[ASN][1000 genomes]
rs152466	0.85[ASN][1000 genomes]
rs187387	0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs190298	0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs193482	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26653	1.00[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs26654	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]
rs26655	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs27527	0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs27645	0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs34737	0.85[ASN][1000 genomes]
rs34750	1.00[CEU][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34751	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34752	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34753	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34755	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs34756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34757	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34759	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34760	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34761	0.90[CHB][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs34762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40090	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs40604	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs42443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs695965	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs28129	CAST	cis	cerebellum	SCAN
rs28129	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs28129	CAST	cis	parietal	SCAN
rs28129	LNPEP	cis	parietal	SCAN
rs28129	ERAP1	cis	Whole Blood	GTEx
rs28129	CHD1	cis	cerebellum	SCAN
rs28129	ERAP2	cis	cerebellum	SCAN
rs28129	ERAP2	cis	lymphoblastoid	seeQTL
rs28129	ERAP2	cis	parietal	SCAN
rs28129	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	chr5:96153000-96156600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:96153000-96156600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr5:96153000-96156600	Weak transcription	Adipose Nuclei	Adipose
17	chr5:96153000-96156600	Weak transcription	HSMM	muscle
18	chr5:96153000-96156800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:96153000-96157200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:96153000-96157200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:96153000-96159200	Weak transcription	Right Atrium	heart
22	chr5:96153200-96155800	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr5:96153200-96155800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr5:96153200-96159200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:96153600-96155800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr5:96153600-96156000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr5:96153600-96156600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr5:96153600-96156600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:96153600-96156800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr5:96153600-96157000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:96153600-96158800	Weak transcription	Fetal Intestine Small	intestine
32	chr5:96153600-96159200	Weak transcription	Osteobl	bone
33	chr5:96153800-96156800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:96154000-96157200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:96154200-96156800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:96154200-96156800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr5:96154200-96158800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:96154400-96156800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr5:96154400-96156800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:96154400-96156800	Weak transcription	Thymus	Thymus
41	chr5:96154400-96157200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr5:96154400-96159400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:96154400-96160400	Enhancers	Dnd41	blood
44	chr5:96155000-96155800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:96155200-96156600	Weak transcription	Primary T cells from cord blood	blood
46	chr5:96155200-96157000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr5:96155200-96157000	Weak transcription	Fetal Thymus	thymus
48	chr5:96155400-96156800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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