Variant report

Variant	rs546936407
Chromosome Location	chr6:13486059-13486060
allele	A/C
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	MXI1	chr6:13484535-13488686	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr6:13486048-13486651	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:13485907-13488270	GM18951	blood:	n/a	n/a
4	POLR2A	chr6:13485921-13488226	GM12892	blood:	n/a	n/a
5	ZNF143	chr6:13485857-13487179	GM12878	blood:	n/a	n/a
6	CHD1	chr6:13485653-13487078	GM12878	blood:	n/a	n/a
7	SIN3A	chr6:13485974-13487504	GM12878	blood:	n/a	chr6:13487441-13487454
8	GTF2F1	chr6:13485867-13486470	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr6:13486042-13486472	GM12892	blood:	n/a	n/a
10	SMC3	chr6:13485901-13488192	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:13486007-13486621	GM12892	blood:	n/a	n/a
12	MAX	chr6:13485823-13488217	K562	blood:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
13	CTCF	chr6:13486040-13486190	GM06990	blood:	n/a	n/a
14	MYC	chr6:13486048-13487263	MCF10A-Er-Src	breast:	n/a	chr6:13486482-13486492
15	POLR2A	chr6:13486036-13486459	GM12878	blood:	n/a	n/a
16	STAT1	chr6:13485831-13486670	GM12878	blood:	n/a	chr6:13486475-13486487
17	TCF7L2	chr6:13486005-13486408	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr6:13485620-13486608	GM12878	blood:	n/a	n/a
19	HA-E2F1	chr6:13485874-13486473	MCF-7	breast:	n/a	n/a
20	SIN3A	chr6:13485845-13488935	H1-hESC	embryonic stem cell:	n/a	chr6:13487441-13487454 chr6:13487722-13487733
21	POLR2A	chr6:13485963-13488286	GM19193	blood:	n/a	n/a
22	BHLHE40	chr6:13485785-13487912	K562	blood:	n/a	chr6:13486336-13486352 chr6:13487437-13487453 chr6:13487232-13487248
23	UBTF	chr6:13486005-13488042	K562	blood:	n/a	n/a
24	TBP	chr6:13485872-13486514	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:13485896-13488307	GM19099	blood:	n/a	n/a
26	ZNF263	chr6:13485651-13488433	HEK293-T-REx	kidney:	n/a	chr6:13486705-13486714
27	POLR2A	chr6:13484266-13486670	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:13485833-13486780	GM12878	blood:	n/a	n/a
29	SMARCB1	chr6:13485896-13487926	Hela-S3	cervix:	n/a	n/a
30	MYC	chr6:13485989-13486711	MCF10A-Er-Src	breast:	n/a	chr6:13486482-13486492
31	NR2F2	chr6:13485698-13487319	K562	blood:	n/a	n/a
32	RUNX3	chr6:13486041-13487337	GM12878	blood:	n/a	n/a
33	POLR2A	chr6:13485760-13488250	GM12878	blood:	n/a	n/a
34	RCOR1	chr6:13485792-13486699	K562	blood:	n/a	n/a
35	TBP	chr6:13485928-13486344	H1-hESC	embryonic stem cell:	n/a	n/a
36	BRCA1	chr6:13485959-13486471	Hela-S3	cervix:	n/a	n/a
37	PML	chr6:13485998-13486675	GM12878	blood:	n/a	n/a
38	MAX	chr6:13486046-13488341	MCF-7	breast:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
39	POLR2A	chr6:13484366-13488416	PBDE	blood:	n/a	n/a
40	MXI1	chr6:13485562-13488187	GM12878	blood:	n/a	n/a
41	TBP	chr6:13486054-13486551	Hela-S3	cervix:	n/a	n/a
42	MAX	chr6:13485718-13488934	HepG2	liver:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
43	WRNIP1	chr6:13485786-13486349	GM12878	blood:	n/a	n/a
44	GATA1	chr6:13483173-13486472	K562	blood:	n/a	chr6:13483771-13483784 chr6:13484564-13484577 chr6:13485418-13485425
45	MAX	chr6:13485998-13488444	A549	lung:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
46	MXI1	chr6:13485337-13488731	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:13484664..13490672-chr6:13572714..13577234,9	K562	blood:
2	chr6:13484393..13490113-chr6:13572102..13578017,14	MCF-7	breast:
3	chr6:13465251..13472690-chr6:13481619..13489131,10	K562	blood:
4	chr6:13326316..13328538-chr6:13485562..13488530,2	MCF-7	breast:
5	chr6:13485388..13489511-chr6:13572660..13577514,13	MCF-7	breast:
6	chr6:13484080..13486133-chr6:13486417..13487997,2	MCF-7	breast:
7	chr6:13325999..13330365-chr6:13484429..13488653,6	MCF-7	breast:
8	chr6:13406818..13408886-chr6:13483840..13488220,5	MCF-7	breast:
9	chr6:13484642..13487748-chr6:13572714..13576594,3	K562	blood:

Variant related genes	Relation type
GFOD1-AS1	TF binding region
ENSG00000124523	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000237786	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3421701	chr6:13485573-13489871	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13483200-13488800	Active TSS	Right Atrium	heart
2	chr6:13483400-13486400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr6:13483400-13487600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:13484200-13488600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:13484400-13486200	Flanking Active TSS	Brain Cingulate Gyrus	brain
6	chr6:13484400-13486400	Flanking Active TSS	HUVEC	blood vessel
7	chr6:13484600-13486200	Flanking Active TSS	Brain Hippocampus Middle	brain
8	chr6:13484600-13487200	Flanking Active TSS	Liver	Liver
9	chr6:13484600-13488400	Active TSS	GM12878-XiMat	blood
10	chr6:13484800-13486200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:13484800-13486200	Flanking Active TSS	NHEK	skin
12	chr6:13484800-13486400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr6:13484800-13487200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr6:13484800-13488400	Active TSS	Right Ventricle	heart
15	chr6:13485000-13486200	Weak transcription	Small Intestine	intestine
16	chr6:13485000-13486600	Active TSS	Colonic Mucosa	Colon
17	chr6:13485000-13488800	Active TSS	Brain Angular Gyrus	brain
18	chr6:13485000-13489600	Active TSS	Rectal Smooth Muscle	rectum
19	chr6:13485200-13488200	Active TSS	Stomach Smooth Muscle	stomach
20	chr6:13485200-13488200	Active TSS	NHLF	lung
21	chr6:13485200-13488600	Active TSS	Left Ventricle	heart
22	chr6:13485200-13488600	Active TSS	A549	lung
23	chr6:13485200-13488800	Active TSS	Brain Anterior Caudate	brain
24	chr6:13485200-13488800	Active TSS	Psoas Muscle	Psoas
25	chr6:13485400-13486200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
26	chr6:13485400-13486200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:13485400-13486200	Flanking Active TSS	Brain Substantia Nigra	brain
28	chr6:13485400-13486200	Bivalent Enhancer	Stomach Mucosa	stomach
29	chr6:13485400-13486400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:13485400-13486400	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr6:13485400-13487200	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:13485400-13487200	Active TSS	Fetal Brain Male	brain
33	chr6:13485400-13487600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr6:13485400-13488600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:13485400-13488600	Active TSS	NHDF-Ad	bronchial
36	chr6:13485600-13486200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:13485600-13486200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr6:13485600-13486200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
39	chr6:13485600-13486200	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
40	chr6:13485600-13486200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr6:13485600-13486200	Flanking Active TSS	NH-A	brain
42	chr6:13485600-13486400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:13485600-13486400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:13485600-13486400	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr6:13485600-13486400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
46	chr6:13485600-13486400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
47	chr6:13485600-13486400	Flanking Active TSS	Dnd41	blood
48	chr6:13485600-13486800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
49	chr6:13485600-13487000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
50	chr6:13485600-13488200	Active TSS	Placenta Amnion	Placenta Amnion

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