Variant report

Variant	rs4550961
Chromosome Location	chr4:76978693-76978694
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:76976399..76978701-chr4:76979279..76981111,2	K562	blood:
2	chr4:76972794..76974652-chr4:76976393..76979116,2	MCF-7	breast:

Extended variants
information (count: 170 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10002099	0.81[EUR][1000 genomes]
rs10003240	0.80[EUR][1000 genomes]
rs10003382	0.80[EUR][1000 genomes]
rs10010920	0.86[EUR][1000 genomes]
rs10014049	0.80[EUR][1000 genomes]
rs10014837	0.80[EUR][1000 genomes]
rs10017431	0.80[EUR][1000 genomes]
rs10021768	0.80[EUR][1000 genomes]
rs10025102	0.80[EUR][1000 genomes]
rs10025181	0.86[EUR][1000 genomes]
rs10033061	0.82[EUR][1000 genomes]
rs10034055	0.83[EUR][1000 genomes]
rs10856873	0.85[EUR][1000 genomes]
rs11097212	0.80[EUR][1000 genomes]
rs11097219	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12502834	0.85[EUR][1000 genomes]
rs12510335	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12647111	0.81[EUR][1000 genomes]
rs13105341	0.83[EUR][1000 genomes]
rs13111790	0.85[EUR][1000 genomes]
rs13113455	0.86[EUR][1000 genomes]
rs13113632	0.85[EUR][1000 genomes]
rs13128319	0.86[EUR][1000 genomes]
rs13130018	0.80[EUR][1000 genomes]
rs13130221	0.80[EUR][1000 genomes]
rs13133745	0.81[EUR][1000 genomes]
rs28433437	0.85[EUR][1000 genomes]
rs28505472	0.84[EUR][1000 genomes]
rs28548768	0.85[EUR][1000 genomes]
rs28642977	0.82[EUR][1000 genomes]
rs28681066	0.83[EUR][1000 genomes]
rs28681694	0.85[EUR][1000 genomes]
rs28757394	0.82[EUR][1000 genomes]
rs28848839	0.82[EUR][1000 genomes]
rs28868672	0.84[EUR][1000 genomes]
rs28896243	0.82[EUR][1000 genomes]
rs3921	0.80[EUR][1000 genomes]
rs4129781	0.82[EUR][1000 genomes]
rs4241578	0.80[EUR][1000 genomes]
rs4241580	0.80[EUR][1000 genomes]
rs4241581	0.82[EUR][1000 genomes]
rs4257674	0.80[EUR][1000 genomes]
rs4276310	0.82[EUR][1000 genomes]
rs4302486	0.80[EUR][1000 genomes]
rs4304003	0.85[EUR][1000 genomes]
rs4309862	0.80[EUR][1000 genomes]
rs4331799	0.80[EUR][1000 genomes]
rs4345214	0.80[EUR][1000 genomes]
rs4356932	0.80[EUR][1000 genomes]
rs4359936	0.85[EUR][1000 genomes]
rs4359937	0.82[EUR][1000 genomes]
rs4373188	0.84[EUR][1000 genomes]
rs4380549	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4386624	0.80[EUR][1000 genomes]
rs4394024	0.81[EUR][1000 genomes]
rs4401475	0.86[EUR][1000 genomes]
rs4406046	0.81[EUR][1000 genomes]
rs4417995	0.80[EUR][1000 genomes]
rs4422436	0.86[EUR][1000 genomes]
rs4432767	0.86[EUR][1000 genomes]
rs4435768	0.85[EUR][1000 genomes]
rs4456983	0.82[EUR][1000 genomes]
rs4478212	0.82[EUR][1000 genomes]
rs4524415	0.82[EUR][1000 genomes]
rs4529084	0.81[EUR][1000 genomes]
rs4532263	0.83[EUR][1000 genomes]
rs4532264	0.84[EUR][1000 genomes]
rs4535358	0.85[EUR][1000 genomes]
rs4541535	0.83[EUR][1000 genomes]
rs4543142	0.82[EUR][1000 genomes]
rs4543147	0.86[EUR][1000 genomes]
rs4547819	0.86[EUR][1000 genomes]
rs4580676	0.80[EUR][1000 genomes]
rs4583787	0.80[EUR][1000 genomes]
rs4593163	0.86[EUR][1000 genomes]
rs4605683	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4610366	0.83[EUR][1000 genomes]
rs4616778	0.86[EUR][1000 genomes]
rs4637430	0.82[EUR][1000 genomes]
rs4643846	0.84[EUR][1000 genomes]
rs4859414	0.80[EUR][1000 genomes]
rs4859415	0.81[EUR][1000 genomes]
rs4859584	0.80[EUR][1000 genomes]
rs4859586	0.80[EUR][1000 genomes]
rs4859587	0.80[EUR][1000 genomes]
rs4859588	0.80[EUR][1000 genomes]
rs4859589	0.81[EUR][1000 genomes]
rs4859590	0.80[EUR][1000 genomes]
rs4859591	0.80[EUR][1000 genomes]
rs4859595	0.80[EUR][1000 genomes]
rs4859597	0.81[EUR][1000 genomes]
rs4859598	0.82[EUR][1000 genomes]
rs4859599	0.82[EUR][1000 genomes]
rs4859600	0.81[EUR][1000 genomes]
rs4859601	0.83[EUR][1000 genomes]
rs4859602	0.83[EUR][1000 genomes]
rs4859603	0.82[EUR][1000 genomes]
rs4859604	0.81[EUR][1000 genomes]
rs4859605	0.81[EUR][1000 genomes]
rs6532093	0.80[EUR][1000 genomes]
rs6532111	0.80[EUR][1000 genomes]
rs6532114	0.81[EUR][1000 genomes]
rs6532121	0.82[EUR][1000 genomes]
rs6532130	0.83[EUR][1000 genomes]
rs6532142	0.83[EUR][1000 genomes]
rs6532143	0.82[EUR][1000 genomes]
rs6532152	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6532153	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6532155	0.85[EUR][1000 genomes]
rs6532156	0.85[EUR][1000 genomes]
rs6532157	0.85[EUR][1000 genomes]
rs6532158	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6532159	0.86[EUR][1000 genomes]
rs6532160	0.86[EUR][1000 genomes]
rs6532161	0.86[EUR][1000 genomes]
rs6532163	0.86[EUR][1000 genomes]
rs6532164	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6532165	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6532166	0.83[EUR][1000 genomes]
rs6532172	0.85[EUR][1000 genomes]
rs6811252	0.83[EUR][1000 genomes]
rs6811301	0.83[EUR][1000 genomes]
rs6811469	0.87[EUR][1000 genomes]
rs6814012	0.80[EUR][1000 genomes]
rs6814817	0.80[EUR][1000 genomes]
rs6816898	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6819597	0.81[EUR][1000 genomes]
rs6825045	0.80[EUR][1000 genomes]
rs6826163	0.85[EUR][1000 genomes]
rs6826398	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6826406	0.88[EUR][1000 genomes]
rs6827767	0.83[EUR][1000 genomes]
rs6828596	0.81[EUR][1000 genomes]
rs6829896	0.83[EUR][1000 genomes]
rs6835736	0.82[EUR][1000 genomes]
rs6837830	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6844097	0.80[EUR][1000 genomes]
rs6845396	0.80[EUR][1000 genomes]
rs6848603	0.89[EUR][1000 genomes]
rs6848620	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6850515	0.84[EUR][1000 genomes]
rs6850760	0.80[EUR][1000 genomes]
rs6852075	0.80[EUR][1000 genomes]
rs6856681	0.86[EUR][1000 genomes]
rs6856958	0.80[EUR][1000 genomes]
rs6857372	0.86[EUR][1000 genomes]
rs7375677	0.81[EUR][1000 genomes]
rs7376624	0.84[EUR][1000 genomes]
rs7376863	0.80[EUR][1000 genomes]
rs7376943	0.86[EUR][1000 genomes]
rs7377856	0.80[EUR][1000 genomes]
rs7436646	0.80[EUR][1000 genomes]
rs7655350	0.86[EUR][1000 genomes]
rs7664354	0.86[EUR][1000 genomes]
rs7665152	0.82[EUR][1000 genomes]
rs7674409	0.82[EUR][1000 genomes]
rs7676265	0.84[EUR][1000 genomes]
rs7683657	0.82[EUR][1000 genomes]
rs7684461	0.82[EUR][1000 genomes]
rs7684889	0.82[EUR][1000 genomes]
rs7688306	0.86[EUR][1000 genomes]
rs7689664	0.82[EUR][1000 genomes]
rs7699624	0.82[EUR][1000 genomes]
rs8878	0.80[EUR][1000 genomes]
rs9884374	0.80[EUR][1000 genomes]
rs9990733	0.82[EUR][1000 genomes]
rs9999755	0.82[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4550961	NAAA	cis	Whole Blood	GTEx
rs4550961	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs4550961	NAAA	cis	Heart Left Ventricle	GTEx
rs4550961	NAAA	cis	Artery Aorta	GTEx
rs4550961	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs4550961	NAAA	cis	Esophagus Muscularis	GTEx
rs4550961	NAAA	cis	Nerve Tibial	GTEx
rs4550961	ART3	cis	Nerve Tibial	GTEx
rs4550961	NAAA	cis	Esophagus Mucosa	GTEx
rs4550961	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs4550961	NAAA	cis	lung	GTEx
rs4550961	ASAHL	cis	multi-tissue	Pritchard
rs4550961	NAAA	cis	Adipose Subcutaneous	GTEx
rs4550961	NAAA	cis	Muscle Skeletal	GTEx
rs4550961	NAAA	cis	Artery Tibial	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76975400-76979200	Weak transcription	HMEC	breast
2	chr4:76976000-76979800	Weak transcription	Fetal Intestine Small	intestine
3	chr4:76976000-76980800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:76976200-76979800	Weak transcription	Fetal Intestine Large	intestine
5	chr4:76976200-76980000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr4:76976400-76980200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:76976600-76979400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:76976600-76979400	Weak transcription	Stomach Mucosa	stomach
9	chr4:76976600-76980600	Weak transcription	Primary B cells from cord blood	blood
10	chr4:76977000-76979400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:76977200-76979400	Weak transcription	NHEK	skin
12	chr4:76977200-76980000	Weak transcription	K562	blood
13	chr4:76977400-76981600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr4:76977800-76978800	Weak transcription	GM12878-XiMat	blood
15	chr4:76978000-76982800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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