Variant report

Variant	rs3777899
Chromosome Location	chr6:134304936-134304937
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	MAFK	chr6:134304543-134305019	K562	blood:	n/a	chr6:134304635-134304644
2	CEBPB	chr6:134304535-134304982	MCF-7	breast:	n/a	n/a
3	REST	chr6:134304511-134304977	HL-60	blood:	n/a	n/a
4	ZMIZ1	chr6:134304678-134304958	K562	blood:	n/a	n/a
5	STAT3	chr6:134304642-134305088	MCF10A-Er-Src	breast:	n/a	chr6:134304777-134304785
6	ATF1	chr6:134304691-134304987	K562	blood:	n/a	n/a
7	CEBPB	chr6:134304564-134304997	A549	lung:	n/a	n/a
8	POLR2A	chr6:134304530-134305046	SK-N-MC	brain:	n/a	n/a
9	MYC	chr6:134304583-134304958	NB4	blood:	n/a	chr6:134304637-134304646
10	CEBPB	chr6:134304638-134304966	K562	blood:	n/a	n/a
11	CEBPB	chr6:134304485-134305073	K562	blood:	n/a	n/a
12	CEBPD	chr6:134304534-134305031	K562	blood:	n/a	n/a
13	TEAD4	chr6:134304564-134305039	K562	blood:	n/a	n/a
14	CEBPB	chr6:134304461-134304983	HCT-116	colon:	n/a	n/a
15	POLR2A	chr6:134304261-134305236	K562	blood:	n/a	n/a
16	POLR2A	chr6:134304236-134305145	K562	blood:	n/a	n/a
17	TBL1XR1	chr6:134304636-134304937	K562	blood:	n/a	n/a
18	JUND	chr6:134304457-134304949	K562	blood:	n/a	chr6:134304638-134304649 chr6:134304636-134304646 chr6:134304637-134304644 chr6:134304637-134304645 chr6:134304637-134304645 chr6:134304636-134304646 chr6:134304636-134304646 chr6:134304636-134304646
19	CEBPB	chr6:134304565-134304987	K562	blood:	n/a	n/a
20	JUN	chr6:134304575-134305022	K562	blood:	n/a	chr6:134304638-134304649 chr6:134304636-134304646 chr6:134304637-134304644 chr6:134304637-134304645 chr6:134304637-134304645 chr6:134304636-134304646 chr6:134304636-134304646 chr6:134304636-134304646
21	GATA2	chr6:134304603-134304987	K562	blood:	n/a	chr6:134304638-134304647
22	CCNT2	chr6:134304652-134305058	K562	blood:	n/a	n/a
23	CEBPB	chr6:134304648-134304941	HepG2	liver:	n/a	n/a
24	CTCF	chr6:134304441-134304996	MCF-7	breast:	n/a	n/a
25	TAL1	chr6:134304636-134304963	K562	blood:	n/a	n/a
26	GATA3	chr6:134304448-134305103	MCF-7	breast:	n/a	chr6:134304638-134304647
27	POLR2A	chr6:134304505-134305092	HL-60	blood:	n/a	n/a
28	STAT5A	chr6:134304595-134305029	K562	blood:	n/a	chr6:134304777-134304785
29	POLR2A	chr6:134304463-134305091	HL-60	blood:	n/a	n/a
30	RCOR1	chr6:134304506-134305005	K562	blood:	n/a	n/a
31	CEBPB	chr6:134304546-134305066	A549	lung:	n/a	n/a
32	POLR2A	chr6:134301184-134306312	K562	blood:	n/a	n/a
33	RCOR1	chr6:134304531-134304950	K562	blood:	n/a	n/a
34	CEBPD	chr6:134304577-134305084	K562	blood:	n/a	n/a
35	NR2F2	chr6:134304603-134304969	K562	blood:	n/a	n/a
36	CEBPB	chr6:134304438-134305129	HCT-116	colon:	n/a	n/a
37	MYC	chr6:134304632-134304956	K562	blood:	n/a	chr6:134304637-134304646
38	EP300	chr6:134304611-134304944	K562	blood:	n/a	chr6:134304637-134304646
39	BHLHE40	chr6:134304621-134305001	K562	blood:	n/a	n/a
40	CEBPB	chr6:134304608-134304991	IMR90	lung:	n/a	n/a
41	CTCF	chr6:134304594-134304997	MCF-7	breast:	n/a	n/a
42	CEBPB	chr6:134304622-134304961	A549	lung:	n/a	n/a
43	POLR2A	chr6:134304574-134304943	K562	blood:	n/a	n/a
44	TRIM28	chr6:134304478-134305014	K562	blood:	n/a	chr6:134304635-134304644
45	CEBPB	chr6:134304531-134305139	MCF-7	breast:	n/a	n/a
46	TEAD4	chr6:134304456-134305132	K562	blood:	n/a	n/a

Variant related genes	Relation type
TBPL1	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10485159	1.00[JPT][hapmap]
rs17063199	1.00[JPT][hapmap]
rs17063210	1.00[JPT][hapmap]
rs17063219	1.00[JPT][hapmap]
rs2220134	0.90[YRI][hapmap]
rs2239558	0.90[EUR][1000 genomes]
rs2268068	1.00[JPT][hapmap]
rs2273097	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34569027	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3777894	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3777896	1.00[CHB][hapmap];0.98[EUR][1000 genomes]
rs3822940	1.00[JPT][hapmap]
rs41286224	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896015	1.00[JPT][hapmap]
rs4896017	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56011629	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57486657	0.96[EUR][1000 genomes]
rs60898069	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6902440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938805	1.00[JPT][hapmap]
rs73548792	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73774169	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73774170	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9483631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9483632	1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs9483634	1.00[CHB][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9483635	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9483639	0.94[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9493768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9493770	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9493771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9493772	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9493773	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9493774	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9493777	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9493778	0.90[YRI][hapmap]
rs9493780	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493783	0.90[YRI][hapmap]
rs9493786	0.96[AFR][1000 genomes];0.98[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34122	chr6:134089019-134378252	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3777899	TBPL1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134276600-134314000	Weak transcription	Thymus	Thymus
2	chr6:134280600-134312200	Weak transcription	Lung	lung
3	chr6:134283200-134305600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:134285000-134316600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:134288200-134311800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:134288400-134306600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:134290800-134316400	Weak transcription	Esophagus	oesophagus
8	chr6:134295000-134313800	Weak transcription	Spleen	Spleen
9	chr6:134295200-134311800	Weak transcription	Brain Germinal Matrix	brain
10	chr6:134297000-134318000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr6:134299400-134307200	Weak transcription	Left Ventricle	heart
12	chr6:134299400-134311800	Weak transcription	Gastric	stomach
13	chr6:134299400-134312000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:134299400-134313200	Weak transcription	Psoas Muscle	Psoas
15	chr6:134299400-134313400	Weak transcription	Aorta	Aorta
16	chr6:134299400-134313800	Weak transcription	Right Ventricle	heart
17	chr6:134299600-134310200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:134299800-134305800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:134299800-134307000	Weak transcription	Ovary	ovary
20	chr6:134299800-134312000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:134299800-134313600	Weak transcription	Fetal Heart	heart
22	chr6:134299800-134314000	Weak transcription	Fetal Brain Male	brain
23	chr6:134300400-134312200	Weak transcription	Small Intestine	intestine
24	chr6:134300400-134315400	Weak transcription	Fetal Intestine Small	intestine
25	chr6:134300600-134305000	Strong transcription	Primary B cells from cord blood	blood
26	chr6:134300600-134305800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr6:134300600-134306800	Weak transcription	Stomach Mucosa	stomach
28	chr6:134300600-134312000	Weak transcription	NHLF	lung
29	chr6:134301000-134312400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:134302000-134308400	Strong transcription	Placenta	Placenta
31	chr6:134302400-134307600	Strong transcription	GM12878-XiMat	blood
32	chr6:134302400-134308200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:134302600-134307800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr6:134302600-134308800	Strong transcription	Liver	Liver
35	chr6:134302600-134309200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:134302800-134305400	Strong transcription	Fetal Kidney	kidney
37	chr6:134302800-134307400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr6:134302800-134308400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:134302800-134308400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:134302800-134308400	Strong transcription	Fetal Lung	lung
41	chr6:134302800-134324000	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:134303000-134305000	Strong transcription	Brain Angular Gyrus	brain
43	chr6:134303000-134305400	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:134303000-134306000	Strong transcription	Brain Anterior Caudate	brain
45	chr6:134303000-134306200	Strong transcription	Fetal Intestine Large	intestine
46	chr6:134303000-134306200	Strong transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:134303000-134306200	Strong transcription	NHDF-Ad	bronchial
48	chr6:134303000-134306600	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr6:134303000-134308000	Strong transcription	HSMM	muscle
50	chr6:134303000-134308600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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