Variant report

Variant	rs246454
Chromosome Location	chr5:96123264-96123265
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96121324..96124158-chr5:96141331..96143363,2	K562	blood:
2	chr5:96119292..96124832-chr5:96125807..96130865,7	K562	blood:
3	chr5:96122964..96125889-chr5:96127442..96130664,3	MCF-7	breast:
4	chr5:96118389..96123506-chr5:96124152..96130865,8	K562	blood:
5	chr5:96122962..96125249-chr5:96269601..96272549,2	MCF-7	breast:
6	chr5:96121088..96123332-chr5:96141994..96144285,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247121	Chromatin interaction
ENSG00000164307	Chromatin interaction
ENSG00000113441	Chromatin interaction
ENSG00000272109	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs149189	0.97[ASN][1000 genomes]
rs151940	0.95[ASN][1000 genomes]
rs151964	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs152280	0.82[ASN][1000 genomes]
rs168674	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs246453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs246456	0.90[AMR][1000 genomes]
rs26489	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs26490	0.93[ASN][1000 genomes]
rs26491	0.97[ASN][1000 genomes]
rs26495	0.97[ASN][1000 genomes]
rs26496	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs26497	0.97[ASN][1000 genomes]
rs26498	0.97[ASN][1000 genomes]
rs26500	0.97[ASN][1000 genomes]
rs26510	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26512	0.96[ASN][1000 genomes]
rs26653	0.86[ASN][1000 genomes]
rs26654	0.86[ASN][1000 genomes]
rs26655	0.86[ASN][1000 genomes]
rs27043	0.86[ASN][1000 genomes]
rs27044	0.86[ASN][1000 genomes]
rs27045	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs27432	0.87[ASN][1000 genomes]
rs27434	0.97[ASN][1000 genomes]
rs27527	0.81[ASN][1000 genomes]
rs27529	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27640	0.97[ASN][1000 genomes]
rs27710	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28119	0.97[ASN][1000 genomes]
rs28333	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28337	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs30185	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs30186	0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs30187	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30334	0.84[ASN][1000 genomes]
rs30376	0.86[ASN][1000 genomes]
rs30378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30379	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30380	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34750	0.85[ASN][1000 genomes]
rs34751	0.85[ASN][1000 genomes]
rs34752	0.84[ASN][1000 genomes]
rs39840	0.86[ASN][1000 genomes]
rs39841	0.85[ASN][1000 genomes]
rs42398	0.86[ASN][1000 genomes]
rs467735	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs469367	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs469674	0.95[ASN][1000 genomes]
rs469758	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469783	0.98[ASN][1000 genomes]
rs695965	0.86[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs246454	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs246454	ERAP1	cis	lung	GTEx
rs246454	ERAP1	cis	Muscle Skeletal	GTEx
rs246454	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs246454	ERAP1	cis	Whole Blood	GTEx
rs246454	ERAP1	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96063000-96126200	Weak transcription	Brain Germinal Matrix	brain
2	chr5:96068400-96138200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr5:96068600-96130000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:96071400-96126600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:96079400-96126600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:96079600-96123600	Strong transcription	Placenta	Placenta
7	chr5:96079600-96126400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:96079600-96126600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:96079600-96126600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:96089200-96137000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:96092800-96126600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:96097400-96130000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr5:96097400-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:96097400-96138400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr5:96097800-96126600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:96097800-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr5:96098000-96129600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:96098000-96137000	Strong transcription	Fetal Lung	lung
19	chr5:96098000-96137600	Strong transcription	Fetal Thymus	thymus
20	chr5:96098200-96128000	Strong transcription	Primary hematopoietic stem cells	blood
21	chr5:96100200-96127000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:96104200-96136400	Strong transcription	Dnd41	blood
23	chr5:96104800-96126600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:96105000-96124400	Weak transcription	Aorta	Aorta
25	chr5:96105000-96127800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:96107600-96129600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:96107800-96138200	Strong transcription	GM12878-XiMat	blood
28	chr5:96108000-96129600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:96110200-96130200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:96110400-96125600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:96110600-96130400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:96111600-96126800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:96112800-96123800	Weak transcription	Brain Angular Gyrus	brain
34	chr5:96113800-96137200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:96114000-96126400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:96114600-96124200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:96114600-96124200	Weak transcription	Pancreas	Pancrea
38	chr5:96114600-96124200	Weak transcription	Right Atrium	heart
39	chr5:96114600-96131000	Weak transcription	Fetal Brain Male	brain
40	chr5:96114800-96124400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:96114800-96126400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:96114800-96131200	Weak transcription	Right Ventricle	heart
43	chr5:96115000-96124200	Weak transcription	Esophagus	oesophagus
44	chr5:96115200-96124200	Weak transcription	Spleen	Spleen
45	chr5:96115200-96141200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr5:96115400-96142000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr5:96115800-96124200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:96116000-96126400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:96116000-96126600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:96116200-96141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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