Variant report

Variant	rs1544777
Chromosome Location	chr5:96314230-96314231
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:96270482..96272119-chr5:96313857..96315491,2	MCF-7	breast:
2	chr5:96311603..96314325-chr5:96315419..96317692,2	K562	blood:
3	chr5:96313535..96315131-chr5:96331601..96334406,2	K562	blood:

Variant related genes	Relation type
ENSG00000247121	Chromatin interaction
ENSG00000113441	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10038651	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10044354	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10051637	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10058476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10077945	0.86[EUR][1000 genomes]
rs10434709	0.85[CEU][hapmap]
rs1046395	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1046396	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10476696	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11135484	0.85[CEU][hapmap]
rs1216566	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1216567	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1216571	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1230358	0.82[JPT][hapmap]
rs12516666	0.86[CEU][hapmap]
rs13167902	0.85[CEU][hapmap]
rs13170029	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13358339	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1363907	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1363908	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1363974	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1363976	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1423357	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1423566	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1477364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1559355	0.86[CEU][hapmap]
rs1820148	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1974871	0.89[CEU][hapmap];0.81[YRI][hapmap]
rs2113050	0.81[CEU][hapmap]
rs2161548	0.89[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2247650	0.83[CEU][hapmap]
rs2278018	0.86[CEU][hapmap]
rs2278019	0.85[CEU][hapmap]
rs2351010	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2351011	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2432141	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs251339	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap]
rs251340	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs251341	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2548224	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2548226	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548516	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2548529	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs2548530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2548532	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2549778	0.82[JPT][hapmap]
rs2549783	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes]
rs2549784	0.84[YRI][hapmap]
rs2549794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2617439	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2617447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27289	0.87[EUR][1000 genomes]
rs27290	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs27293	0.87[EUR][1000 genomes]
rs27295	0.87[EUR][1000 genomes]
rs27298	0.82[EUR][1000 genomes]
rs27300	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs27306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs27436	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs2762	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs27659	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs27660	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs27711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs27712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs27993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs27998	0.83[EUR][1000 genomes]
rs2859491	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2910686	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2910687	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2910788	0.88[EUR][1000 genomes]
rs2910789	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2910793	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2927608	0.81[EUR][1000 genomes]
rs2927609	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3734015	0.86[CEU][hapmap]
rs3797796	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs38029	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38031	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38032	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs38033	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs38034	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs38038	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs38039	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38042	0.83[CEU][hapmap]
rs38043	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs38044	0.88[EUR][1000 genomes]
rs3849749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3909451	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs39602	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs4360063	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4869314	0.86[CEU][hapmap]
rs6556942	0.96[CEU][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap]
rs6859168	0.88[EUR][1000 genomes]
rs6871162	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs6887500	0.88[EUR][1000 genomes]
rs716848	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7703341	0.88[EUR][1000 genomes]
rs7705093	0.81[AMR][1000 genomes]
rs7716222	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7719705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7726445	0.88[EUR][1000 genomes]
rs7731592	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs7733312	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9127	0.92[CEU][hapmap]
rs9314181	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs1544777	ERAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs1544777	ERAP2	cis	Nerve Tibial	GTEx
rs1544777	ERAP2	cis	Artery Aorta	GTEx
rs1544777	ERAP2	cis	Thyroid	GTEx
rs1544777	AC008865.1	cis	Artery Tibial	GTEx
rs1544777	LRAP	cis	normal skin	skin_eQTL
rs1544777	ERAP2	cis	Adipose Subcutaneous	GTEx
rs1544777	LRAP	cis	uninvolved skin	skin_eQTL
rs1544777	ERAP2	cis	Esophagus Mucosa	GTEx
rs1544777	ERAP2	cis	Artery Tibial	GTEx
rs1544777	ERAP2	cis	Heart Left Ventricle	GTEx
rs1544777	ERAP2	cis	Esophagus Muscularis	GTEx
rs1544777	LNPEP	cis	Esophagus Muscularis	GTEx
rs1544777	ERAP2	cis	Stomach	GTEx
rs1544777	ERAP2	cis	Whole Blood	GTEx
rs1544777	LRAP	Cis_1M	lymphoblastoid	RTeQTL
rs1544777	LRAP	cis	lesional skin	skin_eQTL
rs1544777	ERAP2	cis	Muscle Skeletal	GTEx
rs1544777	ERAP2	cis	lung	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96278200-96314400	Weak transcription	Fetal Intestine Large	intestine
2	chr5:96299400-96314800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr5:96299400-96315000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:96299600-96315000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:96299800-96314800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr5:96304600-96315000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:96304600-96315000	Weak transcription	Brain Germinal Matrix	brain
8	chr5:96304600-96315000	Weak transcription	Pancreas	Pancrea
9	chr5:96304600-96329600	Weak transcription	Fetal Brain Female	brain
10	chr5:96304600-96335600	Weak transcription	Stomach Mucosa	stomach
11	chr5:96304800-96314400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:96304800-96314400	Weak transcription	Fetal Intestine Small	intestine
13	chr5:96304800-96314800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:96304800-96315000	Weak transcription	Aorta	Aorta
15	chr5:96304800-96315000	Weak transcription	HepG2	liver
16	chr5:96304800-96315200	Weak transcription	Fetal Kidney	kidney
17	chr5:96304800-96346600	Weak transcription	Lung	lung
18	chr5:96304800-96359600	Weak transcription	Hela-S3	cervix
19	chr5:96305000-96315000	Weak transcription	A549	lung
20	chr5:96305400-96314400	Weak transcription	NH-A	brain
21	chr5:96305400-96314800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:96305400-96314800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:96305400-96314800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:96305400-96314800	Weak transcription	Liver	Liver
25	chr5:96305400-96315000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr5:96305400-96315000	Weak transcription	Brain Angular Gyrus	brain
27	chr5:96305400-96315000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:96305400-96315000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:96305400-96315000	Weak transcription	HUVEC	blood vessel
30	chr5:96305400-96315200	Weak transcription	HMEC	breast
31	chr5:96305400-96315200	Weak transcription	NHEK	skin
32	chr5:96305400-96334200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr5:96306200-96315600	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:96308200-96314800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr5:96308400-96314800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:96308800-96315000	Weak transcription	Adipose Nuclei	Adipose
37	chr5:96309000-96314800	Weak transcription	K562	blood
38	chr5:96309000-96315000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr5:96309600-96314400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr5:96310000-96314400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:96310000-96315000	Weak transcription	Brain Anterior Caudate	brain
42	chr5:96310200-96314400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:96310200-96314400	Weak transcription	Fetal Stomach	stomach
44	chr5:96310200-96314400	Weak transcription	Dnd41	blood
45	chr5:96310200-96314800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:96310200-96314800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:96310200-96315000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr5:96310200-96315000	Weak transcription	Placenta	Placenta
49	chr5:96310200-96315000	Weak transcription	Gastric	stomach
50	chr5:96310200-96315000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links