Variant report

Variant	rs9992952
Chromosome Location	chr4:76898174-76898175
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76896669..76899167-chr4:76911311..76914671,4	MCF-7	breast:
2	chr4:76859621..76862443-chr4:76895909..76899158,3	K562	blood:

Variant related genes	Relation type
ENSG00000138744	Chromatin interaction
ENSG00000198301	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10008757	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10031452	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10336	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11097189	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11732759	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11931349	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11947509	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13111710	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13125558	0.82[EUR][1000 genomes]
rs13126007	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13132564	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13138223	0.89[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1554013	0.81[ASN][1000 genomes]
rs2242471	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242473	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242474	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292533	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28681066	0.83[ASN][1000 genomes]
rs4282209	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4318674	0.81[ASN][1000 genomes]
rs4337760	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859413	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859581	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859582	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4859594	0.81[ASN][1000 genomes]
rs6532078	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6532083	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6826085	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7436021	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7679177	0.83[EUR][1000 genomes]
rs9307050	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995007	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9992952	NAAA	cis	Esophagus Mucosa	GTEx
rs9992952	NAAA	cis	Artery Aorta	GTEx
rs9992952	NAAA	cis	Muscle Skeletal	GTEx
rs9992952	NAAA	cis	Adipose Subcutaneous	GTEx
rs9992952	NAAA	cis	Nerve Tibial	GTEx
rs9992952	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs9992952	NAAA	cis	lung	GTEx
rs9992952	NAAA	cis	Whole Blood	GTEx
rs9992952	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs9992952	ART3	cis	Nerve Tibial	GTEx
rs9992952	ASAHL	cis	multi-tissue	Pritchard
rs9992952	NAAA	cis	Esophagus Muscularis	GTEx
rs9992952	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs9992952	NAAA	cis	Heart Left Ventricle	GTEx
rs9992952	NAAA	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76863000-76903600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr4:76864800-76903000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:76867800-76900000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr4:76867800-76903800	Strong transcription	Fetal Thymus	thymus
5	chr4:76868000-76899800	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:76868000-76903000	Strong transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:76868000-76903000	Strong transcription	Stomach Smooth Muscle	stomach
8	chr4:76868000-76903800	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr4:76868200-76903400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:76868200-76903600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr4:76868400-76903600	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr4:76868400-76903800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:76868400-76903800	Strong transcription	Placenta	Placenta
14	chr4:76869200-76900200	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:76872200-76902800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr4:76882400-76898200	Weak transcription	Aorta	Aorta
17	chr4:76883800-76899800	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr4:76883800-76903000	Strong transcription	Duodenum Mucosa	Duodenum
19	chr4:76884000-76902800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:76884200-76899600	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr4:76884200-76899800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:76884200-76902800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:76884200-76903800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr4:76884600-76899800	Strong transcription	NH-A	brain
25	chr4:76884600-76899800	Strong transcription	Osteobl	bone
26	chr4:76884600-76902800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:76884600-76902800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:76884600-76902800	Strong transcription	Adipose Nuclei	Adipose
29	chr4:76884600-76903400	Strong transcription	HMEC	breast
30	chr4:76884600-76903400	Strong transcription	HSMM	muscle
31	chr4:76884600-76903600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:76884600-76903600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:76884600-76903800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:76884800-76899400	Strong transcription	HUVEC	blood vessel
35	chr4:76884800-76899800	Strong transcription	HepG2	liver
36	chr4:76884800-76900000	Strong transcription	Brain Hippocampus Middle	brain
37	chr4:76884800-76900000	Strong transcription	Left Ventricle	heart
38	chr4:76884800-76900800	Strong transcription	K562	blood
39	chr4:76884800-76902200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:76884800-76902600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:76884800-76903600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:76884800-76903600	Strong transcription	NHEK	skin
43	chr4:76885000-76903000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr4:76885200-76902600	Strong transcription	Fetal Muscle Leg	muscle
45	chr4:76885200-76903800	Strong transcription	Fetal Intestine Large	intestine
46	chr4:76885400-76902600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr4:76885400-76903600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr4:76886400-76899200	Strong transcription	Rectal Smooth Muscle	rectum
49	chr4:76887000-76899000	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:76887000-76902600	Strong transcription	Primary B cells from peripheral blood	blood

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