Variant report

Variant	rs59602208
Chromosome Location	chr3:158360108-158360109
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZMIZ1	chr3:158359967-158360199	K562	blood:	n/a	n/a
2	ZNF143	chr3:158360012-158360206	K562	blood:	n/a	n/a
3	RCOR1	chr3:158359892-158360179	K562	blood:	n/a	n/a
4	TBL1XR1	chr3:158359977-158360194	K562	blood:	n/a	n/a
5	JUND	chr3:158359876-158360594	K562	blood:	n/a	chr3:158360520-158360531
6	CTCF	chr3:158360033-158360243	K562	blood:	n/a	n/a
7	BATF	chr3:158359881-158360126	GM12878	blood:	n/a	n/a
8	GATA2	chr3:158359827-158360354	K562	blood:	n/a	n/a
9	TEAD4	chr3:158359812-158360393	K562	blood:	n/a	n/a
10	EP300	chr3:158359860-158360474	K562	blood:	n/a	n/a
11	MAX	chr3:158359975-158360252	K562	blood:	n/a	n/a
12	NR2F2	chr3:158359757-158360373	K562	blood:	n/a	n/a
13	GATA2	chr3:158359867-158360310	K562	blood:	n/a	n/a
14	NR2F2	chr3:158359821-158360294	K562	blood:	n/a	n/a
15	CCNT2	chr3:158359880-158360273	K562	blood:	n/a	n/a
16	TAL1	chr3:158359884-158360356	K562	blood:	n/a	n/a
17	STAT5A	chr3:158359834-158360312	K562	blood:	n/a	n/a
18	CEBPD	chr3:158359813-158360456	K562	blood:	n/a	n/a
19	CEBPB	chr3:158359903-158360281	K562	blood:	n/a	n/a
20	CBX3	chr3:158359772-158360457	K562	blood:	n/a	n/a
21	TRIM28	chr3:158359712-158360391	K562	blood:	n/a	n/a
22	PML	chr3:158359838-158360314	K562	blood:	n/a	n/a
23	POLR2A	chr3:158359917-158360400	K562	blood:	n/a	n/a
24	TRIM28	chr3:158359819-158360256	K562	blood:	n/a	n/a
25	CEBPB	chr3:158359924-158360285	K562	blood:	n/a	n/a
26	CTCF	chr3:158360100-158360250	K562	blood:	n/a	n/a
27	ATF1	chr3:158359919-158360309	K562	blood:	n/a	n/a
28	MAZ	chr3:158360093-158360322	K562	blood:	n/a	n/a
29	RCOR1	chr3:158359650-158360341	K562	blood:	n/a	n/a
30	TEAD4	chr3:158359710-158360439	K562	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:158358329..158360215-chr3:158360474..158362456,2	MCF-7	breast:
2	chr3:158288507..158290720-chr3:158358983..158360751,2	MCF-7	breast:
3	chr3:158284750..158291147-chr3:158359832..158364955,8	K562	blood:

No data

Variant related genes	Relation type
GFM1	TF binding region
ENSG00000168827	Chromatin interaction
ENSG00000243150	Chromatin interaction
ENSG00000178053	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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10154986	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1038885	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513527	0.94[AMR][1000 genomes];0.93[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	0.84[EUR][1000 genomes]
rs12638363	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13315529	0.88[AMR][1000 genomes];0.94[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	0.80[EUR][1000 genomes]
rs1435639	0.80[EUR][1000 genomes]
rs16829072	0.82[EUR][1000 genomes]
rs16829079	0.82[EUR][1000 genomes]
rs16829116	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829135	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829273	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16829283	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16847130	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847135	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17630223	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17630394	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17630785	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17631016	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17631078	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1864502	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082838	0.88[AMR][1000 genomes];0.91[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];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2363657	0.82[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];1.00[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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4368546	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56321207	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56973279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58034569	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58878998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59492803	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59502510	0.82[EUR][1000 genomes]
rs59527167	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.98[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];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792976	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795710	0.84[EUR][1000 genomes]
rs6797871	0.83[EUR][1000 genomes]
rs6808551	0.89[ASN][1000 genomes]
rs73022714	0.82[EUR][1000 genomes]
rs73022726	0.82[EUR][1000 genomes]
rs73022742	0.85[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];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73024790	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73028934	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73030851	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638518	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7638606	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9830994	0.80[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];0.92[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	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
5	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
6	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
7	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59602208	MLF1	cis	Muscle Skeletal	GTEx
rs59602208	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 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
3	chr3:158359200-158362000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr3:158359600-158360400	Flanking Active TSS	K562	blood
5	chr3:158359800-158360200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:158359800-158361600	Enhancers	Lung	lung
7	chr3:158360000-158360600	Enhancers	Primary T killer memory cells from peripheral blood	blood

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