Variant report

Variant	rs3213809
Chromosome Location	chr5:96127833-96127834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:96123725-96127973	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96127204..96132361-chr5:96142290..96145057,7	MCF-7	breast:
2	chr5:96119292..96124832-chr5:96125807..96130865,7	K562	blood:
3	chr5:96118389..96123506-chr5:96124152..96130865,8	K562	blood:

Variant related genes	Relation type
ERAP1	TF binding region
ENSG00000164307	Chromatin interaction
ENSG00000248734	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10515247	0.83[EUR][1000 genomes]
rs10515248	0.83[EUR][1000 genomes]
rs10515249	0.88[EUR][1000 genomes]
rs10515250	0.87[EUR][1000 genomes]
rs11135480	0.81[EUR][1000 genomes]
rs11738115	0.83[EUR][1000 genomes]
rs11738810	0.85[EUR][1000 genomes]
rs11739020	0.83[EUR][1000 genomes]
rs11740375	0.83[EUR][1000 genomes]
rs11741100	0.83[EUR][1000 genomes]
rs11743410	0.89[EUR][1000 genomes]
rs11745157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11746534	0.89[EUR][1000 genomes]
rs11747148	0.83[EUR][1000 genomes]
rs11747179	0.83[EUR][1000 genomes]
rs11747896	0.83[EUR][1000 genomes]
rs11748519	0.85[EUR][1000 genomes]
rs11749811	0.84[EUR][1000 genomes]
rs11750283	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11750464	0.83[EUR][1000 genomes]
rs11750934	0.85[EUR][1000 genomes]
rs13601	0.81[EUR][1000 genomes]
rs153541	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17402704	0.83[EUR][1000 genomes]
rs17481334	0.83[EUR][1000 genomes]
rs17481759	0.83[EUR][1000 genomes]
rs17481856	0.85[EUR][1000 genomes]
rs2042386	0.81[EUR][1000 genomes]
rs3333	0.82[EUR][1000 genomes]
rs3334	0.82[EUR][1000 genomes]
rs3335	0.82[EUR][1000 genomes]
rs3797805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55773007	0.88[EUR][1000 genomes]
rs55996659	0.83[EUR][1000 genomes]
rs56119802	0.83[EUR][1000 genomes]
rs56213813	0.82[EUR][1000 genomes]
rs56319744	0.89[EUR][1000 genomes]
rs72773917	0.83[EUR][1000 genomes]
rs72773922	0.85[EUR][1000 genomes]
rs72773923	0.85[EUR][1000 genomes]
rs72773932	0.85[EUR][1000 genomes]
rs72773942	0.85[EUR][1000 genomes]
rs72773947	0.88[EUR][1000 genomes]
rs72773950	0.88[EUR][1000 genomes]
rs72773968	0.89[EUR][1000 genomes]
rs72773969	0.87[EUR][1000 genomes]
rs72773981	0.81[EUR][1000 genomes]
rs72773986	0.81[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3213809	ERAP1	cis	cerebellar cortex	BrainEAC
rs3213809	ERAP1	cis	temporal cortex	BrainEAC
rs3213809	ERAP1	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96068400-96138200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr5:96068600-96130000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr5:96089200-96137000	Strong transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:96097400-96130000	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr5:96097400-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:96097400-96138400	Strong transcription	Primary B cells from peripheral blood	blood
7	chr5:96097800-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:96098000-96129600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:96098000-96137000	Strong transcription	Fetal Lung	lung
10	chr5:96098000-96137600	Strong transcription	Fetal Thymus	thymus
11	chr5:96098200-96128000	Strong transcription	Primary hematopoietic stem cells	blood
12	chr5:96104200-96136400	Strong transcription	Dnd41	blood
13	chr5:96107600-96129600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr5:96107800-96138200	Strong transcription	GM12878-XiMat	blood
15	chr5:96108000-96129600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:96110200-96130200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:96110600-96130400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr5:96113800-96137200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:96114600-96131000	Weak transcription	Fetal Brain Male	brain
20	chr5:96114800-96131200	Weak transcription	Right Ventricle	heart
21	chr5:96115200-96141200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr5:96115400-96142000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:96116200-96141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr5:96117400-96137000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr5:96117600-96131800	Strong transcription	Liver	Liver
26	chr5:96119000-96130800	Weak transcription	Psoas Muscle	Psoas
27	chr5:96119000-96142000	Weak transcription	A549	lung
28	chr5:96120800-96129800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:96120800-96130000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:96121600-96128600	Weak transcription	HSMM	muscle
31	chr5:96123600-96137000	Strong transcription	Primary B cells from cord blood	blood
32	chr5:96123800-96128000	Strong transcription	Thymus	Thymus
33	chr5:96123800-96137200	Strong transcription	Adipose Nuclei	Adipose
34	chr5:96124000-96130400	Strong transcription	Primary T cells from cord blood	blood
35	chr5:96124600-96131000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:96124600-96136800	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:96124800-96129600	Weak transcription	Colonic Mucosa	Colon
38	chr5:96124800-96130000	Weak transcription	Aorta	Aorta
39	chr5:96124800-96130000	Weak transcription	Esophagus	oesophagus
40	chr5:96125200-96128000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:96125800-96128000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr5:96125800-96128800	Weak transcription	Hela-S3	cervix
43	chr5:96126000-96131600	Weak transcription	Fetal Kidney	kidney
44	chr5:96126000-96133200	Strong transcription	HepG2	liver
45	chr5:96126800-96131800	Weak transcription	Fetal Brain Female	brain
46	chr5:96126800-96135600	Weak transcription	Fetal Heart	heart
47	chr5:96126800-96142800	Weak transcription	Brain Germinal Matrix	brain
48	chr5:96127000-96128000	Strong transcription	Left Ventricle	heart
49	chr5:96127000-96135400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:96127000-96140400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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