Variant report

Variant	rs56011629
Chromosome Location	chr6:134273355-134273356
allele	C/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	MYC	chr6:134273160-134273733	MCF-7	breast:	n/a	n/a
2	CHD2	chr6:134273108-134274868	Hela-S3	cervix:	n/a	chr6:134273783-134273792
3	YY1	chr6:134273013-134273360	GM12891	blood:	n/a	n/a
4	POLR2A	chr6:134273095-134273395	A549	lung:	n/a	n/a
5	TCF7L2	chr6:134272872-134273746	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr6:134273016-134274744	PFSK-1	brain:	n/a	n/a
7	MXI1	chr6:134272992-134274682	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:134273033-134273753	ECC-1	luminal epithelium:	n/a	n/a
9	JUND	chr6:134273119-134274571	K562	blood:	n/a	n/a
10	POLR2A	chr6:134273010-134274668	K562	blood:	n/a	n/a
11	MXI1	chr6:134273207-134274556	H1-hESC	embryonic stem cell:	n/a	n/a
12	NFIC	chr6:134272987-134274455	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:134272881-134274732	GM18951	blood:	n/a	n/a
14	NFIC	chr6:134273001-134274602	GM12878	blood:	n/a	n/a
15	BHLHE40	chr6:134272994-134274455	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:134273142-134273367	A549	lung:	n/a	n/a
17	MXI1	chr6:134273009-134273677	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr6:134273043-134273810	GM12891	blood:	n/a	n/a
19	MAX	chr6:134273055-134273795	Hela-S3	cervix:	n/a	n/a
20	YY1	chr6:134272917-134273635	HepG2	liver:	n/a	n/a
21	ZBTB7A	chr6:134273010-134273565	K562	blood:	n/a	n/a
22	MAX	chr6:134272996-134274912	HepG2	liver:	n/a	chr6:134274197-134274207 chr6:134274440-134274449 chr6:134274689-134274699
23	ZBTB7A	chr6:134273053-134273551	K562	blood:	n/a	n/a
24	POLR2A	chr6:134273099-134273876	Gliobla	brain:	n/a	n/a
25	HEY1	chr6:134272931-134274541	HepG2	liver:	n/a	chr6:134274513-134274528 chr6:134274519-134274534
26	CTCF	chr6:134273335-134273394	GM12892	blood:	n/a	n/a
27	GABPA	chr6:134273165-134274730	SK-N-SH	brain:	n/a	chr6:134274638-134274647 chr6:134274199-134274208
28	POLR2A	chr6:134272923-134273780	GM12878	blood:	n/a	n/a
29	POLR2A	chr6:134273021-134274934	HepG2	liver:	n/a	n/a
30	ZNF384	chr6:134272870-134274460	K562	blood:	n/a	chr6:134272950-134272958
31	HEY1	chr6:134273046-134273473	K562	blood:	n/a	n/a
32	MAZ	chr6:134272821-134274582	GM12878	blood:	n/a	chr6:134274197-134274207 chr6:134274440-134274449
33	POLR2A	chr6:134273154-134273853	MCF-7	breast:	n/a	n/a
34	EBF1	chr6:134273177-134273781	GM12878	blood:	n/a	chr6:134273381-134273392 chr6:134273566-134273579 chr6:134273353-134273366
35	POLR2A	chr6:134273291-134273438	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr6:134273080-134273793	A549	lung:	n/a	n/a
37	POLR2A	chr6:134273090-134274786	MCF-7	breast:	n/a	n/a
38	POLR2A	chr6:134273063-134274682	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr6:134273004-134273882	GM12892	blood:	n/a	n/a
40	RAD21	chr6:134272967-134273432	H1-hESC	embryonic stem cell:	n/a	chr6:134273327-134273340
41	HMGN3	chr6:134273128-134273624	K562	blood:	n/a	n/a
42	RCOR1	chr6:134272997-134274928	K562	blood:	n/a	n/a
43	POLR2A	chr6:134272978-134274741	GM12892	blood:	n/a	n/a
44	POLR2A	chr6:134272999-134274613	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:134272371-134274622	GM12891	blood:	n/a	n/a
46	POLR2A	chr6:134273028-134275015	K562	blood:	n/a	n/a
47	CTCF	chr6:134273078-134273509	K562	blood:	n/a	chr6:134273431-134273444
48	MAX	chr6:134272969-134273845	ECC-1	luminal epithelium:	n/a	n/a
49	ZBTB7A	chr6:134273267-134273565	HepG2	liver:	n/a	n/a
50	RAD21	chr6:134273048-134273386	IMR90	lung:	n/a	chr6:134273327-134273340

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133132887..133135811-chr6:134273188..134277510,5	K562	blood:
2	chr6:134273314..134277341-chr6:134371733..134374606,4	K562	blood:

Variant related genes	Relation type
TBPL1	TF binding region
ENSG00000112306	Chromatin interaction
ENSG00000146411	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2239558	0.92[EUR][1000 genomes]
rs2273097	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34569027	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777894	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777896	0.96[EUR][1000 genomes]
rs3777899	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41286224	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4896017	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57486657	0.95[EUR][1000 genomes]
rs60898069	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6902440	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73548792	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73774169	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73774170	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9483631	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9483632	0.90[EUR][1000 genomes]
rs9483634	0.98[EUR][1000 genomes]
rs9483635	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9483639	0.96[EUR][1000 genomes]
rs9493768	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493770	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs9493771	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493772	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9493773	0.98[EUR][1000 genomes]
rs9493774	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9493777	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9493780	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9493786	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	esv1840176	chr6:134268822-134274297	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
3	esv3387903	chr6:134272809-134276207	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56011629	TBPL1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:134272400-134274000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr6:134272400-134275200	Active TSS	Fetal Brain Female	brain
3	chr6:134272400-134275200	Active TSS	Fetal Kidney	kidney
4	chr6:134272400-134275200	Active TSS	Stomach Smooth Muscle	stomach
5	chr6:134272400-134275400	Active TSS	Aorta	Aorta
6	chr6:134272600-134273800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr6:134272600-134274400	Active TSS	Brain Germinal Matrix	brain
8	chr6:134272600-134274800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:134272600-134275000	Active TSS	Primary T cells fromperipheralblood	blood
10	chr6:134272600-134275200	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr6:134272600-134275200	Active TSS	Brain Angular Gyrus	brain
12	chr6:134272600-134275200	Active TSS	Colonic Mucosa	Colon
13	chr6:134272600-134275200	Active TSS	Fetal Intestine Small	intestine
14	chr6:134272600-134275200	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr6:134272600-134275200	Active TSS	Rectal Smooth Muscle	rectum
16	chr6:134272600-134275200	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr6:134272600-134275200	Active TSS	HMEC	breast
18	chr6:134272600-134275600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:134272600-134275600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr6:134272600-134275600	Active TSS	Ovary	ovary
21	chr6:134272600-134276200	Active TSS	Right Atrium	heart
22	chr6:134272800-134273400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:134272800-134273400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:134272800-134273600	Bivalent/Poised TSS	Fetal Thymus	thymus
25	chr6:134272800-134273800	Flanking Bivalent TSS/Enh	Dnd41	blood
26	chr6:134272800-134273800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr6:134272800-134274200	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr6:134272800-134274400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:134272800-134274800	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr6:134272800-134275000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:134272800-134275000	Active TSS	Brain Cingulate Gyrus	brain
32	chr6:134272800-134275000	Active TSS	Fetal Heart	heart
33	chr6:134272800-134275000	Active TSS	Fetal Intestine Large	intestine
34	chr6:134272800-134275000	Active TSS	Fetal Muscle Leg	muscle
35	chr6:134272800-134275000	Active TSS	Placenta	Placenta
36	chr6:134272800-134275000	Active TSS	Osteobl	bone
37	chr6:134272800-134275200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:134272800-134275200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:134272800-134275200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr6:134272800-134275200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:134272800-134275200	Active TSS	Muscle Satellite Cultured Cells	--
42	chr6:134272800-134275200	Active TSS	Brain Hippocampus Middle	brain
43	chr6:134272800-134275200	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr6:134272800-134275200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:134272800-134275200	Active TSS	Duodenum Mucosa	Duodenum
46	chr6:134272800-134275200	Active TSS	Fetal Stomach	stomach
47	chr6:134272800-134275200	Active TSS	Psoas Muscle	Psoas
48	chr6:134272800-134275200	Active TSS	Right Ventricle	heart
49	chr6:134272800-134275200	Active TSS	HSMM	muscle
50	chr6:134272800-134275200	Active TSS	NHDF-Ad	bronchial

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