Variant report

Variant	rs13125558
Chromosome Location	chr4:76852585-76852586
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:76846485..76850652-chr4:76851327..76855093,5	K562	blood:
2	chr4:76850798..76854400-chr4:76859062..76863095,5	MCF-7	breast:
3	chr4:76852145..76854131-chr4:76857580..76859399,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138744	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10008757	0.96[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10014837	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs10017431	1.00[JPT][hapmap]
rs10017484	1.00[JPT][hapmap]
rs10021768	1.00[JPT][hapmap]
rs10031452	1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs10856875	1.00[JPT][hapmap]
rs11097189	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11097212	1.00[JPT][hapmap]
rs11732759	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11931349	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11947509	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13111710	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13126007	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13128319	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs13132564	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2242471	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2242473	0.96[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2242474	0.96[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2273	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2292533	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3921	1.00[JPT][hapmap]
rs4129781	1.00[JPT][hapmap]
rs4241579	1.00[JPT][hapmap]
rs4257674	1.00[JPT][hapmap]
rs4282209	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs4302486	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4304003	1.00[JPT][hapmap]
rs4333205	1.00[JPT][hapmap]
rs4337760	0.83[EUR][1000 genomes]
rs4380549	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4386624	1.00[JPT][hapmap]
rs4406046	1.00[JPT][hapmap]
rs4417995	1.00[JPT][hapmap]
rs4422436	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4512021	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4535358	1.00[JPT][hapmap]
rs4616778	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4619915	1.00[JPT][hapmap]
rs4859413	0.96[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs4859414	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4859415	1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap]
rs4859416	1.00[JPT][hapmap]
rs4859581	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs4859582	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs4859584	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4859586	1.00[JPT][hapmap]
rs4859587	1.00[JPT][hapmap]
rs4859588	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4859590	1.00[JPT][hapmap]
rs4859591	1.00[JPT][hapmap]
rs4859595	1.00[JPT][hapmap]
rs4859608	1.00[JPT][hapmap]
rs5005114	1.00[JPT][hapmap]
rs6532078	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs6532083	1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs6532114	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs6532121	1.00[JPT][hapmap];0.80[MEX][hapmap]
rs6532142	1.00[JPT][hapmap]
rs6532157	1.00[JPT][hapmap]
rs6814012	1.00[JPT][hapmap]
rs6814817	1.00[JPT][hapmap]
rs6816898	1.00[JPT][hapmap]
rs6819597	1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs6826085	1.00[CEU][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6840980	1.00[JPT][hapmap]
rs6844097	1.00[JPT][hapmap]
rs6845396	1.00[JPT][hapmap]
rs6850760	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7436021	0.83[EUR][1000 genomes]
rs7670789	1.00[JPT][hapmap]
rs7674409	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs7679177	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7684461	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs8878	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs9307050	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs9884374	1.00[JPT][hapmap]
rs9992952	0.82[EUR][1000 genomes]
rs9995007	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3353539	chr4:76530136-76993859	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised 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	51 gene(s)	inside rSNPs	diseases
2	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1004627	chr4:76793910-76999584	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs13125558	NAAA	cis	lung	GTEx
rs13125558	SLC6A20	trans	multi-tissue	Pritchard
rs13125558	NAAA	cis	Adipose Subcutaneous	GTEx
rs13125558	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs13125558	NAAA	cis	parietal	SCAN
rs13125558	NAAA	cis	cerebellum	SCAN
rs13125558	NAAA	cis	Muscle Skeletal	GTEx
rs13125558	CXCL11	cis	multi-tissue	Pritchard
rs13125558	NAAA	cis	lymphoblastoid	seeQTL
rs13125558	CXCL10	cis	lymphoblastoid	seeQTL
rs13125558	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs13125558	NAAA	cis	Nerve Tibial	GTEx
rs13125558	NAAA	cis	Esophagus Muscularis	GTEx
rs13125558	NAAA	cis	Artery Aorta	GTEx
rs13125558	NAAA	cis	Esophagus Mucosa	GTEx
rs13125558	ASAHL	cis	multi-tissue	Pritchard
rs13125558	NAAA	cis	Whole Blood	GTEx
rs13125558	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs13125558	ART3	cis	Nerve Tibial	GTEx
rs13125558	NAAA	cis	Artery Tibial	GTEx
rs13125558	NAAA	cis	Heart Left Ventricle	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76832600-76859000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr4:76833800-76856400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:76833800-76860800	Weak transcription	Fetal Heart	heart
4	chr4:76835000-76859400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:76835000-76859600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:76835200-76859800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:76837000-76857200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:76837000-76860200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr4:76837200-76860800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr4:76837200-76860800	Weak transcription	HSMM	muscle
11	chr4:76837600-76858400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:76837600-76859200	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:76837600-76860800	Weak transcription	Fetal Kidney	kidney
14	chr4:76837800-76860800	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:76837800-76860800	Weak transcription	NH-A	brain
16	chr4:76838000-76857600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:76838200-76852600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr4:76838600-76860800	Weak transcription	NHLF	lung
19	chr4:76839000-76860400	Weak transcription	HUVEC	blood vessel
20	chr4:76839400-76860800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:76839600-76859200	Weak transcription	Brain Substantia Nigra	brain
22	chr4:76839800-76860800	Weak transcription	Psoas Muscle	Psoas
23	chr4:76839800-76860800	Weak transcription	HMEC	breast
24	chr4:76841800-76857400	Weak transcription	Osteobl	bone
25	chr4:76841800-76860800	Weak transcription	Brain Germinal Matrix	brain
26	chr4:76842000-76855800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:76842000-76857400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:76842000-76860400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:76842400-76860800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:76842600-76860800	Weak transcription	Pancreas	Pancrea
31	chr4:76843000-76860600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:76843000-76860800	Weak transcription	Thymus	Thymus
33	chr4:76843000-76860800	Weak transcription	NHEK	skin
34	chr4:76843400-76859800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr4:76843400-76860000	Weak transcription	A549	lung
36	chr4:76843400-76861000	Weak transcription	Small Intestine	intestine
37	chr4:76845000-76852600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr4:76845400-76860800	Weak transcription	Right Ventricle	heart
39	chr4:76845600-76860800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:76846000-76857000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:76846000-76860800	Weak transcription	HSMMtube	muscle
42	chr4:76846400-76855800	Strong transcription	Fetal Intestine Small	intestine
43	chr4:76847200-76855800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:76848800-76855800	Strong transcription	Liver	Liver
45	chr4:76849000-76853800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:76849200-76852600	Strong transcription	Primary T cells from cord blood	blood
47	chr4:76849200-76852800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr4:76849200-76853000	Strong transcription	Primary B cells from peripheral blood	blood
49	chr4:76849200-76853200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr4:76849200-76853200	Strong transcription	Left Ventricle	heart

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