Variant report

Variant	rs6783879
Chromosome Location	chr3:158427589-158427590
allele	G/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	PBX3	chr3:158427209-158427946	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr3:158427172-158428024	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:158427376-158427757	SK-N-SH	brain:	n/a	n/a
4	RAD21	chr3:158427395-158427843	IMR90	lung:	n/a	n/a
5	CTCF	chr3:158427460-158427610	AG09319	gingival:	n/a	n/a
6	POLR2A	chr3:158427239-158427970	U87	brain:	n/a	n/a
7	JUND	chr3:158427220-158427993	SK-N-SH	brain:	n/a	chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427619-158427627 chr3:158427659-158427667
8	JUND	chr3:158427270-158427955	SK-N-SH	brain:	n/a	chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427619-158427627 chr3:158427659-158427667
9	POLR2A	chr3:158427498-158427672	K562	blood:	n/a	n/a
10	JUND	chr3:158427202-158427994	SK-N-SH	brain:	n/a	chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427619-158427627 chr3:158427659-158427667
11	POLR2A	chr3:158427115-158427905	U87	brain:	n/a	n/a
12	CTCF	chr3:158427440-158427590	AG10803	skin:	n/a	n/a
13	RCOR1	chr3:158427539-158427842	K562	blood:	n/a	n/a
14	YY1	chr3:158427355-158427874	SK-N-SH_RA	brain:	n/a	n/a
15	STAT3	chr3:158427474-158427764	MCF10A-Er-Src	breast:	n/a	chr3:158427490-158427502
16	FOSL2	chr3:158427211-158427983	SK-N-SH	brain:	n/a	chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427619-158427627 chr3:158427659-158427667
17	STAT3	chr3:158427415-158427816	MCF10A-Er-Src	breast:	n/a	chr3:158427490-158427502
18	GATA3	chr3:158427238-158428025	SK-N-SH	brain:	n/a	n/a
19	GATA3	chr3:158427130-158427995	SK-N-SH	brain:	n/a	n/a
20	EP300	chr3:158427576-158427678	K562	blood:	n/a	n/a
21	TAF1	chr3:158427433-158427805	SK-N-SH	brain:	n/a	n/a
22	MXI1	chr3:158427184-158427958	IMR90	lung:	n/a	n/a
23	EP300	chr3:158427215-158427888	SK-N-SH_RA	brain:	n/a	n/a
24	FOS	chr3:158427416-158427809	MCF10A-Er-Src	breast:	n/a	chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427657-158427668 chr3:158427619-158427627 chr3:158427659-158427667
25	SIN3AK20	chr3:158427292-158427891	SK-N-SH	brain:	n/a	n/a
26	YY1	chr3:158427267-158427867	SK-N-SH_RA	brain:	n/a	n/a
27	JUND	chr3:158427515-158427892	K562	blood:	n/a	chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427619-158427627 chr3:158427659-158427667
28	POLR2A	chr3:158427115-158427899	U87	brain:	n/a	n/a
29	NFIC	chr3:158427203-158428002	SK-N-SH	brain:	n/a	n/a
30	MAFK	chr3:158427381-158427839	IMR90	lung:	n/a	chr3:158427585-158427596 chr3:158427585-158427596 chr3:158427586-158427597 chr3:158427584-158427598
31	POLR2A	chr3:158427265-158427914	SK-N-SH	brain:	n/a	n/a
32	REST	chr3:158427503-158427823	SK-N-SH	brain:	n/a	n/a
33	TEAD4	chr3:158427179-158428005	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr3:158427388-158427845	Hela-S3	cervix:	n/a	n/a
35	TEAD4	chr3:158427398-158427987	SK-N-SH	brain:	n/a	n/a
36	RCOR1	chr3:158426909-158428040	IMR90	lung:	n/a	n/a
37	FOSL2	chr3:158427368-158427952	SK-N-SH	brain:	n/a	chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427619-158427627 chr3:158427659-158427667
38	POLR2A	chr3:158427257-158427960	IMR90	lung:	n/a	n/a
39	POLR2A	chr3:158427187-158427989	PBDE	blood:	n/a	n/a
40	FOS	chr3:158427487-158427868	MCF10A-Er-Src	breast:	n/a	chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427657-158427668 chr3:158427619-158427627 chr3:158427659-158427667
41	TCF12	chr3:158427128-158428008	SK-N-SH	brain:	n/a	n/a
42	MAX	chr3:158427374-158427887	SK-N-SH	brain:	n/a	chr3:158427445-158427454
43	EP300	chr3:158427166-158427973	SK-N-SH	brain:	n/a	chr3:158427919-158427933
44	MAFK	chr3:158427451-158427842	K562	blood:	n/a	chr3:158427585-158427596 chr3:158427585-158427596 chr3:158427586-158427597 chr3:158427584-158427598
45	POLR2A	chr3:158427219-158427914	U87	brain:	n/a	n/a
46	MYC	chr3:158427494-158427789	MCF10A-Er-Src	breast:	n/a	n/a
47	RAD21	chr3:158427300-158427866	SK-N-SH_RA	brain:	n/a	n/a
48	MAX	chr3:158427356-158427920	A549	lung:	n/a	chr3:158427445-158427454
49	FOS	chr3:158427446-158427819	MCF10A-Er-Src	breast:	n/a	chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427658-158427668 chr3:158427657-158427668 chr3:158427619-158427627 chr3:158427659-158427667
50	MAFF	chr3:158427515-158427831	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:158422890..158425062-chr3:158426331..158429823,3	MCF-7	breast:
2	chr3:158415231..158418143-chr3:158424169..158428339,3	MCF-7	breast:
3	chr3:158423141..158424731-chr3:158426844..158428477,2	K562	blood:

Variant related genes	Relation type
RARRES1	TF binding region
ENSG00000118849	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1047366	0.83[CEU][hapmap]
rs12639052	0.83[CEU][hapmap]
rs17699456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864507	0.83[CEU][hapmap]
rs2303909	0.84[CEU][hapmap]
rs2364927	0.83[ASN][1000 genomes]
rs2566346	0.96[ASN][1000 genomes]
rs3851362	0.83[CEU][hapmap]
rs4680460	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4875	0.84[CEU][hapmap]
rs57932243	0.82[ASN][1000 genomes]
rs61794797	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441224	0.85[ASN][1000 genomes]
rs6772483	0.84[CEU][hapmap]
rs6800914	0.84[CEU][hapmap]
rs6803047	0.84[CEU][hapmap]
rs6804249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7618110	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621897	0.84[CEU][hapmap]
rs7635993	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs8455	0.83[CEU][hapmap]
rs891464	0.84[CEU][hapmap]
rs9819567	0.84[CEU][hapmap]
rs9825696	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9840571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9861938	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs9863103	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs9866134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	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
4	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
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1007141	chr3:158415840-158433128	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6783879	MLF1	cis	Esophagus Mucosa	GTEx
rs6783879	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs6783879	MLF1	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390400-158428600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr3:158390800-158429400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:158390800-158430200	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:158390800-158430400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:158390800-158430800	Weak transcription	Right Ventricle	heart
6	chr3:158390800-158430800	Weak transcription	Stomach Mucosa	stomach
7	chr3:158390800-158432800	Weak transcription	Spleen	Spleen
8	chr3:158390800-158444200	Weak transcription	Gastric	stomach
9	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:158391000-158429200	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:158391000-158430600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:158397000-158429200	Weak transcription	Ovary	ovary
14	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
16	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:158400600-158429000	Weak transcription	Brain Substantia Nigra	brain
18	chr3:158403600-158438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:158408400-158430200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:158408400-158443000	Weak transcription	HepG2	liver
21	chr3:158409000-158429800	Weak transcription	Small Intestine	intestine
22	chr3:158409800-158439000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr3:158410800-158430400	Weak transcription	Fetal Thymus	thymus
24	chr3:158411600-158439400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:158412200-158440800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:158412400-158439200	Weak transcription	Fetal Kidney	kidney
27	chr3:158415000-158440800	Weak transcription	Colonic Mucosa	Colon
28	chr3:158415800-158429600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr3:158416000-158430800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:158416800-158428600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:158417600-158440600	Weak transcription	Aorta	Aorta
32	chr3:158420600-158429400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr3:158421000-158427800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:158421600-158431200	Strong transcription	Primary T cells from cord blood	blood
35	chr3:158421800-158435600	Strong transcription	Fetal Intestine Small	intestine
36	chr3:158422600-158429400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr3:158422800-158427600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:158423200-158431800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:158423800-158438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:158424000-158427800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr3:158424200-158446000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:158424600-158429200	Weak transcription	Psoas Muscle	Psoas
43	chr3:158424800-158427800	Strong transcription	Liver	Liver
44	chr3:158425000-158427800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:158425000-158427800	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:158425000-158429400	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:158425000-158431000	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr3:158425200-158427800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:158425200-158429000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:158425200-158431000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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