Variant report

Variant	rs62401365
Chromosome Location	chr6:27441530-27441531
allele	A/G
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	MXI1	chr6:27439093-27441591	SK-N-SH	brain:	n/a	chr6:27440736-27440751
2	HA-E2F1	chr6:27440167-27441551	MCF-7	breast:	n/a	chr6:27440692-27440699 chr6:27440707-27440716 chr6:27440692-27440699 chr6:27440709-27440718 chr6:27440692-27440699
3	ZNF384	chr6:27440725-27441633	GM12878	blood:	n/a	n/a
4	PML	chr6:27439862-27441599	K562	blood:	n/a	n/a
5	GTF3C2	chr6:27441011-27441678	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr6:27440157-27441552	HepG2	liver:	n/a	n/a
7	ZNF384	chr6:27441423-27441850	K562	blood:	n/a	n/a
8	MAZ	chr6:27439873-27441699	IMR90	lung:	n/a	chr6:27440736-27440745
9	HCFC1	chr6:27439191-27441674	Hela-S3	cervix:	n/a	n/a
10	NR2F2	chr6:27439731-27441642	K562	blood:	n/a	n/a
11	GTF3C2	chr6:27440601-27442024	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26158037..26160369-chr6:27440864..27442625,2	K562	blood:
2	chr6:27356277..27359093-chr6:27439899..27443040,4	MCF-7	breast:
3	chr6:27114670..27118026-chr6:27440668..27442830,6	K562	blood:
4	chr6:27261990..27263611-chr6:27441334..27443428,2	K562	blood:
5	chr6:27148927..27151021-chr6:27440997..27443273,2	K562	blood:
6	chr6:27112142..27119511-chr6:27439134..27442830,9	K562	blood:
7	chr6:27279187..27280995-chr6:27439360..27441808,2	MCF-7	breast:
8	chr6:27354651..27357206-chr6:27439212..27442131,3	K562	blood:
9	chr6:27143738..27145587-chr6:27441019..27442990,2	K562	blood:

Variant related genes	Relation type
ZNF184	TF binding region
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000158553	Chromatin interaction
ENSG00000124613	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs1014227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10452601	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10484396	0.83[ASN][1000 genomes]
rs10484397	0.86[ASN][1000 genomes]
rs10484398	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10807023	0.86[ASN][1000 genomes]
rs10807024	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10807025	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946916	0.85[EUR][1000 genomes]
rs10946919	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10946920	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10946921	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946931	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10946932	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10946933	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11970336	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197858	0.86[ASN][1000 genomes]
rs12199110	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12200018	0.86[ASN][1000 genomes]
rs12205189	0.82[ASN][1000 genomes]
rs12206045	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12212288	0.82[ASN][1000 genomes]
rs12212293	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12213598	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215117	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12524409	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525544	0.82[ASN][1000 genomes]
rs12528904	0.82[ASN][1000 genomes]
rs12529839	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12529840	0.83[ASN][1000 genomes]
rs13201443	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201965	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201985	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13207099	0.82[ASN][1000 genomes]
rs13212050	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13215560	0.92[ASN][1000 genomes]
rs13217162	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13217248	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13217798	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13220155	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1569566	0.86[ASN][1000 genomes]
rs1883216	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2049944	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2049945	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2092120	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2092121	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2092122	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2103557	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2142705	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179154	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205831	0.83[ASN][1000 genomes]
rs2206253	0.83[ASN][1000 genomes]
rs2206254	0.86[ASN][1000 genomes]
rs2235252	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2235254	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2272814	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272815	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2272816	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294308	0.92[ASN][1000 genomes]
rs2294309	0.91[ASN][1000 genomes]
rs2893916	0.83[ASN][1000 genomes]
rs2893917	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34185469	0.82[ASN][1000 genomes]
rs35394453	0.99[ASN][1000 genomes]
rs4478400	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711151	0.81[ASN][1000 genomes]
rs4711153	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713101	0.82[ASN][1000 genomes]
rs4713104	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713105	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4713106	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713107	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713109	0.92[ASN][1000 genomes]
rs55705181	0.84[ASN][1000 genomes]
rs57647048	0.86[ASN][1000 genomes]
rs6456784	0.82[ASN][1000 genomes]
rs6456785	0.82[ASN][1000 genomes]
rs6456786	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6456788	0.92[ASN][1000 genomes]
rs6456789	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6456791	0.85[ASN][1000 genomes]
rs6650992	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6899780	0.86[ASN][1000 genomes]
rs6899950	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6903282	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6904844	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6908086	0.86[ASN][1000 genomes]
rs6911865	0.92[ASN][1000 genomes]
rs6914542	0.86[ASN][1000 genomes]
rs6914585	0.86[ASN][1000 genomes]
rs6918131	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6918794	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6920010	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920408	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920733	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921071	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926142	0.83[ASN][1000 genomes]
rs6928314	0.82[ASN][1000 genomes]
rs6929812	0.82[ASN][1000 genomes]
rs6931659	0.88[ASN][1000 genomes]
rs6933354	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6938689	0.81[EUR][1000 genomes]
rs726830	0.94[ASN][1000 genomes]
rs7509	0.98[ASN][1000 genomes]
rs760880	0.86[ASN][1000 genomes]
rs764460	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs764461	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7741031	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743443	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7743465	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7744110	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7745380	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747283	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7747444	0.83[ASN][1000 genomes]
rs7748366	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7750795	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754086	0.82[ASN][1000 genomes]
rs7754678	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7754724	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7754977	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7756216	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756377	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7764070	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764634	0.95[ASN][1000 genomes]
rs7771590	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7771598	0.82[ASN][1000 genomes]
rs7772160	0.96[ASN][1000 genomes]
rs7774613	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7776338	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468134	0.85[AFR][1000 genomes]
rs9468140	0.92[ASN][1000 genomes]
rs9468141	0.92[ASN][1000 genomes]
rs979352	0.86[ASN][1000 genomes]
rs979353	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
3	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv883508	chr6:27434220-27455625	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62401365	ZNF391	cis	lung	GTEx
rs62401365	ZNF391	cis	Nerve Tibial	GTEx
rs62401365	ZNF391	cis	Esophagus Muscularis	GTEx
rs62401365	ZNF391	cis	Heart Left Ventricle	GTEx
rs62401365	ZNF391	cis	Skin Sun Exposed Lower leg	GTEx
rs62401365	BRP44	trans	lymphoblastoid	RTeQTL
rs62401365	ZNF391	cis	Artery Tibial	GTEx
rs62401365	ZNF391	cis	Esophagus Mucosa	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27437400-27441800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr6:27438600-27442000	Active TSS	GM12878-XiMat	blood
3	chr6:27438600-27442000	Active TSS	K562	blood
4	chr6:27438800-27441600	Active TSS	Brain Cingulate Gyrus	brain
5	chr6:27438800-27441600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr6:27438800-27441800	Active TSS	Fetal Lung	lung
7	chr6:27438800-27442200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr6:27438800-27442200	Active TSS	Brain Angular Gyrus	brain
9	chr6:27439000-27441800	Active TSS	Fetal Kidney	kidney
10	chr6:27439000-27441800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr6:27439000-27441800	Active TSS	HSMM	muscle
12	chr6:27439000-27442800	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr6:27439200-27441600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:27439200-27441600	Active TSS	Brain Hippocampus Middle	brain
15	chr6:27439200-27441800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:27439200-27441800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:27439200-27441800	Active TSS	iPS-15b Cell Line	embryonic stem cell
18	chr6:27439200-27441800	Active TSS	Fetal Stomach	stomach
19	chr6:27439200-27441800	Active TSS	Stomach Smooth Muscle	stomach
20	chr6:27439200-27442000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:27439200-27442200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:27439200-27442200	Active TSS	NH-A	brain
23	chr6:27439200-27442400	Active TSS	A549	lung
24	chr6:27439200-27442600	Active TSS	H1 Cell Line	embryonic stem cell
25	chr6:27439400-27441600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr6:27439400-27441600	Active TSS	HSMMtube	muscle
27	chr6:27439400-27441600	Active TSS	NHDF-Ad	bronchial
28	chr6:27439400-27441800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:27439400-27441800	Active TSS	NHEK	skin
30	chr6:27439400-27442000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr6:27439400-27442000	Active TSS	Fetal Intestine Large	intestine
32	chr6:27439400-27442200	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr6:27439400-27442200	Active TSS	Fetal Intestine Small	intestine
34	chr6:27439400-27442400	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr6:27439600-27441600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:27439600-27441600	Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr6:27439600-27441600	Active TSS	Fetal Muscle Trunk	muscle
38	chr6:27439600-27441800	Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:27439600-27441800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr6:27439600-27441800	Active TSS	Brain Anterior Caudate	brain
41	chr6:27439600-27441800	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr6:27439600-27441800	Active TSS	Rectal Smooth Muscle	rectum
43	chr6:27439600-27441800	Active TSS	Osteobl	bone
44	chr6:27439600-27442000	Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr6:27439600-27442000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:27439600-27442000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:27439600-27442000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:27439600-27442200	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr6:27439600-27442200	Active TSS	Hela-S3	cervix
50	chr6:27439600-27442200	Active TSS	NHLF	lung

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