Variant report

Variant	rs25866
Chromosome Location	chr5:96131037-96131038
allele	G/T
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	chr5:96130367-96133704	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96130139..96133072-chr5:96133533..96136124,4	K562	blood:
2	chr5:96127204..96132361-chr5:96142290..96145057,7	MCF-7	breast:
3	chr5:96130627..96133603-chr5:96137872..96139471,2	K562	blood:
4	chr5:96129620..96132075-chr5:96136043..96138068,3	MCF-7	breast:

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

Extended variants
information (count: 22 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs149173	0.90[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs153541	0.84[CEU][hapmap]
rs26511	0.97[ASN][1000 genomes]
rs27036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27528	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27895	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs28046	0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs30333	1.00[ASW][hapmap];0.88[CHB][hapmap];0.97[LWK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3734016	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs998509	0.81[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs25866	CTD-2260A17.1	cis	Skin Sun Exposed Lower leg	GTEx
rs25866	CTD-2260A17.1	cis	Artery Tibial	GTEx
rs25866	ERAP1	cis	lymphoblastoid	seeQTL
rs25866	CAST	cis	multi-tissue	Pritchard
rs25866	CTD-2260A17.1	cis	Artery Aorta	GTEx
rs25866	CTD-2260A17.1	cis	Thyroid	GTEx
rs25866	CTD-2260A17.1	cis	lung	GTEx
rs25866	ERAP1	cis	parietal	SCAN

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	chr5:96089200-96137000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr5:96097400-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:96097400-96138400	Strong transcription	Primary B cells from peripheral blood	blood
5	chr5:96097800-96131800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:96098000-96137000	Strong transcription	Fetal Lung	lung
7	chr5:96098000-96137600	Strong transcription	Fetal Thymus	thymus
8	chr5:96104200-96136400	Strong transcription	Dnd41	blood
9	chr5:96107800-96138200	Strong transcription	GM12878-XiMat	blood
10	chr5:96113800-96137200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:96114800-96131200	Weak transcription	Right Ventricle	heart
12	chr5:96115200-96141200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr5:96115400-96142000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:96116200-96141600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:96117400-96137000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr5:96117600-96131800	Strong transcription	Liver	Liver
17	chr5:96119000-96142000	Weak transcription	A549	lung
18	chr5:96123600-96137000	Strong transcription	Primary B cells from cord blood	blood
19	chr5:96123800-96137200	Strong transcription	Adipose Nuclei	Adipose
20	chr5:96124600-96136800	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:96126000-96131600	Weak transcription	Fetal Kidney	kidney
22	chr5:96126000-96133200	Strong transcription	HepG2	liver
23	chr5:96126800-96131800	Weak transcription	Fetal Brain Female	brain
24	chr5:96126800-96135600	Weak transcription	Fetal Heart	heart
25	chr5:96126800-96142800	Weak transcription	Brain Germinal Matrix	brain
26	chr5:96127000-96135400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:96127000-96140400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr5:96127000-96142600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:96127000-96142800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:96127200-96131200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:96127200-96131200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:96127200-96131400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:96127200-96131800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:96127200-96132200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr5:96127200-96137000	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:96127200-96137000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr5:96127200-96137400	Strong transcription	Placenta	Placenta
38	chr5:96127200-96139600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr5:96127200-96139800	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr5:96127400-96131200	Weak transcription	Stomach Mucosa	stomach
41	chr5:96127400-96131800	Weak transcription	HSMMtube	muscle
42	chr5:96127400-96132000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr5:96127400-96133000	Strong transcription	NHLF	lung
44	chr5:96127400-96135800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr5:96127400-96136800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr5:96127400-96142600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr5:96127400-96142600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:96127400-96142600	Weak transcription	NH-A	brain
49	chr5:96127600-96133000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:96127600-96133600	Strong transcription	NHEK	skin

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