Variant report

Variant	rs58878998
Chromosome Location	chr3:158358648-158358649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:158358206-158359939	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:158358616-158358666	HCM	heart:	n/a
2	chr3:158358616-158358666	SK-N-SH	brain:	n/a
3	chr3:158358616-158358666	HCT-116	colon:	n/a
4	chr3:158358616-158358666	HEEpiC	esophagus:	n/a
5	chr3:158358616-158358666	PFSK-1	brain:	n/a
6	chr3:158358616-158358666	H1-hESC	embryonic stem cell:	embryo
7	chr3:158358616-158358666	ECC-1	luminal epithelium:	n/a
8	chr3:158358616-158358666	Jurkat	blood:	n/a
9	chr3:158358616-158358666	HMEC	breast:	n/a
10	chr3:158358616-158358666	HPAEpiC	pulmonary alveolar:	n/a
11	chr3:158358616-158358666	AG09309	skin:	n/a
12	chr3:158358616-158358666	BJ	skin:	n/a
13	chr3:158358616-158358666	RPTEC	kidney:	n/a
14	chr3:158358616-158358666	HCF	heart:	n/a
15	chr3:158358616-158358666	SK-N-MC	brain:	n/a
16	chr3:158358616-158358666	IMR90	lung:	fetal
17	chr3:158358616-158358666	MCF10A-Er-Src	breast:	n/a
18	chr3:158358616-158358666	AG04450	lung:	fetal
19	chr3:158358616-158358666	BE2_C	brain:	n/a
20	chr3:158358616-158358666	NT2-D1	testis:	n/a
21	chr3:158358616-158358666	GM12878	blood:	n/a
22	chr3:158358616-158358666	NHDF-neo	bronchial:	n/a
23	chr3:158358616-158358666	GM12892	blood:	n/a
24	chr3:158358616-158358666	Hepatocyte	liver:	n/a
25	chr3:158358616-158358666	NH-A	brain:	n/a
26	chr3:158358616-158358666	CMK	blood:	n/a
27	chr3:158358616-158358666	HRPEpiC	eye:	n/a
28	chr3:158358616-158358666	HRE	kidney:	n/a
29	chr3:158358616-158358666	GM12891	blood:	n/a
30	chr3:158358616-158358666	HL-60	blood:	n/a
31	chr3:158358616-158358666	NB4	blood:	n/a
32	chr3:158358616-158358666	SAEC	small airway:	n/a
33	chr3:158358616-158358666	HNPCEpiC	eye:	n/a
34	chr3:158358616-158358666	MCF-7	breast:	n/a
35	chr3:158358616-158358666	ProgFib	skin:	n/a
36	chr3:158358616-158358666	U87	brain:	n/a
37	chr3:158358616-158358666	HepG2	liver:	n/a
38	chr3:158358616-158358666	LNCaP	prostate:	n/a
39	chr3:158358616-158358666	NHBE	bronchial:	n/a
40	chr3:158358616-158358666	HEK293	kidney:	embryo
41	chr3:158358616-158358666	HIPEpiC	eye:	n/a
42	chr3:158358616-158358666	SKMC	muscle:	n/a
43	chr3:158358616-158358666	GM06990	blood:	n/a
44	chr3:158358616-158358666	PrEC	prostate:	n/a
45	chr3:158358616-158358666	SK-N-SH_RA	brain:	n/a
46	chr3:158358616-158358666	AoSMC	blood vessel:	n/a
47	chr3:158358616-158358666	HRCEpiC	kidney:	n/a
48	chr3:158358616-158358666	AG09319	gingival:	n/a
49	chr3:158358616-158358666	AG04449	skin:	fetal
50	chr3:158358616-158358666	HCPEpiC	choroid plexus:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158358329..158360215-chr3:158360474..158362456,2	MCF-7	breast:

No data

Variant related genes	Relation type
GFM1	TF binding region
GFM1	CpG island
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10154981	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10154986	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1038885	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513527	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12106885	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107742	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486595	0.85[EUR][1000 genomes]
rs12638363	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13315529	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318109	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435638	0.81[EUR][1000 genomes]
rs1435639	0.81[EUR][1000 genomes]
rs16829072	0.83[EUR][1000 genomes]
rs16829079	0.83[EUR][1000 genomes]
rs16829116	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829135	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829273	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829283	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16847130	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847135	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17630223	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17630394	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17630785	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17631016	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17631078	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864502	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082838	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2115942	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291594	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2363657	0.83[EUR][1000 genomes]
rs2364273	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28856044	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806642	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3817373	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41272617	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368546	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56321207	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56973279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58034569	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59492803	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59502510	0.83[EUR][1000 genomes]
rs59527167	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59602208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59973861	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61107068	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61292339	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779054	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792976	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795710	0.85[EUR][1000 genomes]
rs6797871	0.84[EUR][1000 genomes]
rs6808551	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73022714	0.83[EUR][1000 genomes]
rs73022726	0.83[EUR][1000 genomes]
rs73022742	0.86[EUR][1000 genomes]
rs73022762	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73022770	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73022798	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73024783	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73024790	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73028934	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030851	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638518	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7638606	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9830994	0.81[EUR][1000 genomes]
rs9849437	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872682	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881679	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3399089	chr3:158356055-158410094	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58878998	MLF1	cis	Muscle Skeletal	GTEx
rs58878998	GFM1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158358000-158362000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:158358600-158362000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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