Variant report

Variant	rs27660
Chromosome Location	chr5:96347775-96347776
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96347498..96349401-chr5:96373632..96375200,2	MCF-7	breast:
2	chr5:96344374..96348016-chr5:96348687..96353038,8	K562	blood:
3	chr5:96270349..96273666-chr5:96345721..96348885,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113441	Chromatin interaction
ENSG00000247121	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10038651	0.87[EUR][1000 genomes]
rs10044354	0.87[EUR][1000 genomes]
rs10051637	0.85[EUR][1000 genomes]
rs10058476	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10077945	0.83[EUR][1000 genomes]
rs1046395	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1046396	0.85[EUR][1000 genomes]
rs10476696	0.87[EUR][1000 genomes]
rs1216566	0.89[EUR][1000 genomes]
rs1216567	0.89[EUR][1000 genomes]
rs1216571	0.89[EUR][1000 genomes]
rs13170029	0.85[EUR][1000 genomes]
rs13358339	0.87[EUR][1000 genomes]
rs1363907	0.88[EUR][1000 genomes]
rs1363908	0.88[EUR][1000 genomes]
rs1363974	0.87[EUR][1000 genomes]
rs1363976	0.86[EUR][1000 genomes]
rs1423357	0.87[EUR][1000 genomes]
rs1423566	0.85[EUR][1000 genomes]
rs1477364	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1544777	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1820148	0.88[EUR][1000 genomes]
rs2161548	0.87[EUR][1000 genomes]
rs2351010	0.88[EUR][1000 genomes]
rs2351011	0.88[EUR][1000 genomes]
rs2432141	0.84[EUR][1000 genomes]
rs251340	0.88[EUR][1000 genomes]
rs251341	0.87[EUR][1000 genomes]
rs2548224	0.82[EUR][1000 genomes]
rs2548226	0.84[EUR][1000 genomes]
rs2548516	0.82[EUR][1000 genomes]
rs2548530	0.88[EUR][1000 genomes]
rs2548532	0.88[EUR][1000 genomes]
rs2549783	0.88[EUR][1000 genomes]
rs2549794	0.88[EUR][1000 genomes]
rs2617439	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2617447	0.89[EUR][1000 genomes]
rs27289	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27290	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27293	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27294	0.80[EUR][1000 genomes]
rs27295	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs27298	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs27300	0.90[EUR][1000 genomes]
rs27302	0.85[EUR][1000 genomes]
rs27306	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27307	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27436	0.93[EUR][1000 genomes]
rs2762	0.85[EUR][1000 genomes]
rs27659	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs27711	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27712	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27993	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27998	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2859491	0.88[EUR][1000 genomes]
rs2910686	0.80[EUR][1000 genomes]
rs2910687	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2910788	0.85[EUR][1000 genomes]
rs2910789	0.85[EUR][1000 genomes]
rs2910793	0.88[EUR][1000 genomes]
rs2927609	0.88[EUR][1000 genomes]
rs31398	0.80[EUR][1000 genomes]
rs3797796	0.86[EUR][1000 genomes]
rs38029	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs38030	0.80[EUR][1000 genomes]
rs38031	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38032	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38033	0.88[EUR][1000 genomes]
rs38034	0.88[EUR][1000 genomes]
rs38038	0.94[EUR][1000 genomes]
rs38039	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38043	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs38044	0.93[EUR][1000 genomes]
rs3849749	0.88[EUR][1000 genomes]
rs3909451	0.87[EUR][1000 genomes]
rs39602	0.93[EUR][1000 genomes]
rs4360063	0.88[EUR][1000 genomes]
rs6859168	0.86[EUR][1000 genomes]
rs6871162	0.85[EUR][1000 genomes]
rs6887500	0.85[EUR][1000 genomes]
rs716848	0.89[EUR][1000 genomes]
rs7703341	0.85[EUR][1000 genomes]
rs7716222	0.88[EUR][1000 genomes]
rs7719705	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7726445	0.85[EUR][1000 genomes]
rs7731592	0.85[EUR][1000 genomes]
rs7733312	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9314181	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	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
5	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
6	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

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs27660	ERAP2	cis	lung	GTEx
rs27660	ERAP2	cis	Thyroid	GTEx
rs27660	ERAP2	cis	Artery Aorta	GTEx
rs27660	LNPEP	cis	Artery Tibial	GTEx
rs27660	ERAP2	cis	Whole Blood	GTEx
rs27660	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs27660	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs27660	LNPEP	cis	Esophagus Muscularis	GTEx
rs27660	ERAP2	cis	Esophagus Muscularis	GTEx
rs27660	ERAP2	cis	Heart Left Ventricle	GTEx
rs27660	ERAP2	cis	Stomach	GTEx
rs27660	ERAP2	cis	Esophagus Mucosa	GTEx
rs27660	AC008865.1	cis	Artery Tibial	GTEx
rs27660	ERAP2	cis	Adipose Subcutaneous	GTEx
rs27660	ERAP2	cis	Nerve Tibial	GTEx
rs27660	ERAP2	cis	Artery Tibial	GTEx
rs27660	ERAP2	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96304800-96359600	Weak transcription	Hela-S3	cervix
2	chr5:96314000-96360200	Weak transcription	Fetal Brain Male	brain
3	chr5:96315400-96374800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:96315600-96353400	Weak transcription	Pancreas	Pancrea
5	chr5:96315600-96358600	Weak transcription	Brain Substantia Nigra	brain
6	chr5:96316000-96360000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr5:96320000-96357600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:96322200-96348600	Weak transcription	Fetal Kidney	kidney
9	chr5:96322200-96349800	Weak transcription	Psoas Muscle	Psoas
10	chr5:96322400-96353600	Weak transcription	Right Ventricle	heart
11	chr5:96322400-96358600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:96322400-96359600	Weak transcription	Gastric	stomach
13	chr5:96329800-96358800	Weak transcription	Brain Germinal Matrix	brain
14	chr5:96330000-96359800	Weak transcription	Aorta	Aorta
15	chr5:96330400-96359400	Weak transcription	Fetal Brain Female	brain
16	chr5:96330600-96353600	Weak transcription	Esophagus	oesophagus
17	chr5:96331600-96356200	Weak transcription	Fetal Stomach	stomach
18	chr5:96331600-96357800	Weak transcription	Spleen	Spleen
19	chr5:96331800-96349800	Weak transcription	HSMM	muscle
20	chr5:96333600-96374000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:96333800-96372800	Strong transcription	Placenta	Placenta
22	chr5:96334800-96351800	Weak transcription	A549	lung
23	chr5:96335800-96359600	Weak transcription	Stomach Mucosa	stomach
24	chr5:96336000-96352400	Weak transcription	NHEK	skin
25	chr5:96336200-96357800	Weak transcription	Fetal Intestine Small	intestine
26	chr5:96336600-96355400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr5:96336600-96359400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:96336600-96359400	Weak transcription	Colonic Mucosa	Colon
29	chr5:96336800-96349400	Weak transcription	NHLF	lung
30	chr5:96336800-96350200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:96336800-96350600	Weak transcription	HSMMtube	muscle
32	chr5:96336800-96355200	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:96337000-96349800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr5:96337600-96355200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:96340000-96351600	Weak transcription	Ovary	ovary
36	chr5:96340600-96359800	Weak transcription	NHDF-Ad	bronchial
37	chr5:96340800-96349800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr5:96340800-96359800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:96341000-96358800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:96341200-96349800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr5:96341400-96348600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr5:96341400-96349400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:96341400-96350600	Weak transcription	Thymus	Thymus
44	chr5:96341600-96349200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:96342600-96374400	Weak transcription	HepG2	liver
46	chr5:96342800-96348800	Weak transcription	Osteobl	bone
47	chr5:96342800-96349600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:96342800-96351400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:96342800-96358600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:96343000-96350600	Weak transcription	Brain Cingulate Gyrus	brain

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