Variant report

Variant	rs17288671
Chromosome Location	chr4:76932001-76932002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr4:76931971-76933216	H1-hESC	embryonic stem cell:	n/a	chr4:76933136-76933147

Variant related genes	Relation type
ART3	TF binding region
CXCL9	TF binding region

Extended variants
information (count: 189 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:186)

rs_ID	r²[population]
rs10000130	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10002099	0.90[EUR][1000 genomes]
rs10002290	0.82[EUR][1000 genomes]
rs10003240	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10003382	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10010920	0.89[EUR][1000 genomes]
rs10014049	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10014837	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10017431	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10021768	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025102	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025302	0.88[EUR][1000 genomes]
rs10025412	0.83[EUR][1000 genomes]
rs10031452	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10033061	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10034055	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10856873	0.90[EUR][1000 genomes]
rs11097212	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11097219	0.89[EUR][1000 genomes]
rs12502834	0.88[EUR][1000 genomes]
rs12510335	0.85[EUR][1000 genomes]
rs12647111	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13111790	0.90[EUR][1000 genomes]
rs13113455	0.90[EUR][1000 genomes]
rs13113632	0.90[EUR][1000 genomes]
rs13128319	0.89[EUR][1000 genomes]
rs13130018	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13130221	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1554013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28433437	0.90[EUR][1000 genomes]
rs28494900	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28505472	0.89[EUR][1000 genomes]
rs28548768	0.90[EUR][1000 genomes]
rs28642977	0.88[EUR][1000 genomes]
rs28681066	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28681694	0.90[EUR][1000 genomes]
rs28848839	0.85[EUR][1000 genomes]
rs28868672	0.81[EUR][1000 genomes]
rs28896243	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3921	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4129781	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4241578	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4241579	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4241580	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4241581	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4257674	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4276310	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4282209	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4302486	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4304003	0.88[EUR][1000 genomes]
rs4309862	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4318674	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4331799	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4345214	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4356932	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4359936	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4359937	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4371639	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4373188	0.87[EUR][1000 genomes]
rs4380549	0.89[EUR][1000 genomes]
rs4386624	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4394024	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4401475	0.89[EUR][1000 genomes]
rs4406046	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4417995	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4422436	0.89[EUR][1000 genomes]
rs4432767	0.89[EUR][1000 genomes]
rs4435768	0.87[EUR][1000 genomes]
rs4456983	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4478212	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4512021	0.82[AMR][1000 genomes]
rs4524415	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4532263	0.86[EUR][1000 genomes]
rs4535358	0.88[EUR][1000 genomes]
rs4541535	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4543142	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4543147	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4547819	0.89[EUR][1000 genomes]
rs4580676	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4583787	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4593163	0.89[EUR][1000 genomes]
rs4610366	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4616778	0.89[EUR][1000 genomes]
rs4619915	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4637430	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4643846	0.84[EUR][1000 genomes]
rs4859414	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859415	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859584	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859586	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859587	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859588	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859589	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4859590	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4859591	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859594	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859595	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859597	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859598	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859599	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4859600	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859601	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859602	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4859603	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859604	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4859605	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4859606	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6532078	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6532083	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532086	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6532093	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6532101	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6532103	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6532105	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6532111	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6532114	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6532121	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6532130	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6532142	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6532143	0.89[EUR][1000 genomes]
rs6532155	0.88[EUR][1000 genomes]
rs6532156	0.88[EUR][1000 genomes]
rs6532157	0.88[EUR][1000 genomes]
rs6532158	0.89[EUR][1000 genomes]
rs6532159	0.89[EUR][1000 genomes]
rs6532160	0.89[EUR][1000 genomes]
rs6532161	0.89[EUR][1000 genomes]
rs6532163	0.89[EUR][1000 genomes]
rs6532166	0.86[EUR][1000 genomes]
rs6532172	0.88[EUR][1000 genomes]
rs6811252	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6811301	0.90[EUR][1000 genomes]
rs6811469	0.86[EUR][1000 genomes]
rs6814012	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6814817	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6816898	0.85[EUR][1000 genomes]
rs6819597	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819920	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6825045	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6826163	0.90[EUR][1000 genomes]
rs6826398	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6826406	0.82[EUR][1000 genomes]
rs6827128	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6827767	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6828596	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6829896	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6833788	0.84[AMR][1000 genomes]
rs6835736	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6837830	0.89[EUR][1000 genomes]
rs6844097	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6845154	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6845198	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6845396	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6848603	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6848620	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6850515	0.88[EUR][1000 genomes]
rs6850760	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6852075	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6856681	0.89[EUR][1000 genomes]
rs6856958	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6857372	0.89[EUR][1000 genomes]
rs7375677	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7376624	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7376943	0.83[EUR][1000 genomes]
rs7377856	0.88[EUR][1000 genomes]
rs73825703	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7436646	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7655350	0.89[EUR][1000 genomes]
rs7664354	0.89[EUR][1000 genomes]
rs7665152	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7670789	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7674409	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7676265	0.83[EUR][1000 genomes]
rs7677924	0.81[EUR][1000 genomes]
rs7683657	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7684461	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7684889	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7688306	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7689664	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7699624	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8878	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9884374	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9990733	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9992010	0.83[EUR][1000 genomes]
rs9999755	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[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
rs17288671	CXCL10	Cis_1M	lymphoblastoid	RTeQTL
rs17288671	NAAA	cis	Skin Sun Exposed Lower leg	GTEx
rs17288671	ART3	cis	Nerve Tibial	GTEx
rs17288671	NAAA	cis	Heart Left Ventricle	GTEx
rs17288671	NAAA	cis	Whole Blood	GTEx
rs17288671	NAAA	cis	lung	GTEx
rs17288671	ASAHL	cis	multi-tissue	Pritchard
rs17288671	NAAA	cis	Adipose Subcutaneous	GTEx
rs17288671	NAAA	cis	Artery Tibial	GTEx
rs17288671	NAAA	cis	Esophagus Mucosa	GTEx
rs17288671	NAAA	cis	Muscle Skeletal	GTEx
rs17288671	NAAA	cis	Nerve Tibial	GTEx
rs17288671	ASAHL	Cis_1M	lymphoblastoid	RTeQTL
rs17288671	NAAA	cis	Artery Aorta	GTEx
rs17288671	NAAA	cis	Esophagus Muscularis	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:76912400-76932200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:76928800-76932400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:76928800-76932400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:76928800-76932600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:76929000-76932400	Weak transcription	HMEC	breast
6	chr4:76929000-76932400	Weak transcription	NHEK	skin
7	chr4:76929000-76934200	Weak transcription	Fetal Intestine Small	intestine
8	chr4:76929200-76932600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:76929200-76932600	Weak transcription	Liver	Liver
10	chr4:76930800-76932400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:76931600-76933000	Enhancers	Placenta	Placenta
12	chr4:76931800-76932800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:76931800-76933000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:76931800-76933000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:76932000-76932600	Enhancers	GM12878-XiMat	blood
16	chr4:76932000-76933000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:76932000-76934400	Enhancers	Cortex derived primary cultured neurospheres	brain

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