Variant report

Variant	rs6458872
Chromosome Location	chr6:13488244-13488245
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	RCOR1	chr6:13487746-13488441	GM12878	blood:	n/a	n/a
2	MXI1	chr6:13484535-13488686	SK-N-SH	brain:	n/a	n/a
3	ELK1	chr6:13488203-13488387	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:13485907-13488270	GM18951	blood:	n/a	n/a
5	POLR2A	chr6:13486837-13488588	HUVEC	blood vessel:	n/a	n/a
6	TAF1	chr6:13486897-13488362	ECC-1	luminal epithelium:	n/a	n/a
7	SP4	chr6:13487960-13488477	H1-hESC	embryonic stem cell:	n/a	chr6:13488105-13488121
8	STAT5A	chr6:13487994-13488568	GM12878	blood:	n/a	n/a
9	MAX	chr6:13486184-13488812	GM12878	blood:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
10	POLR2A	chr6:13487358-13488298	HUVEC	blood vessel:	n/a	n/a
11	CEBPB	chr6:13488145-13488606	MCF-7	breast:	n/a	n/a
12	POLR2A	chr6:13486331-13488405	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr6:13487558-13488296	GM12891	blood:	n/a	n/a
14	POLR2A	chr6:13488227-13488246	MCF-7	breast:	n/a	n/a
15	MAX	chr6:13486122-13489098	ECC-1	luminal epithelium:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
16	MAX	chr6:13486151-13488394	HCT-116	colon:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
17	MAX	chr6:13486178-13489004	ECC-1	luminal epithelium:	n/a	chr6:13487342-13487351 chr6:13486482-13486492
18	POLR2A	chr6:13488062-13488246	A549	lung:	n/a	n/a
19	MAX	chr6:13487487-13488444	SK-N-SH	brain:	n/a	n/a
20	ZNF143	chr6:13487602-13488392	GM12878	blood:	n/a	chr6:13487890-13487908
21	CEBPB	chr6:13488222-13488530	Hela-S3	cervix:	n/a	n/a
22	SIN3A	chr6:13485845-13488935	H1-hESC	embryonic stem cell:	n/a	chr6:13487441-13487454 chr6:13487722-13487733
23	POLR2A	chr6:13485963-13488286	GM19193	blood:	n/a	n/a
24	MAX	chr6:13487719-13489223	H1-hESC	embryonic stem cell:	n/a	chr6:13489179-13489195
25	E2F4	chr6:13487447-13488244	MCF10A-Er-Src	breast:	n/a	chr6:13487750-13487760 chr6:13488144-13488158
26	POLR2A	chr6:13487545-13488680	HEK293	kidney:	n/a	n/a
27	E2F6	chr6:13486464-13489361	H1-hESC	embryonic stem cell:	n/a	chr6:13488882-13488892 chr6:13488624-13488633 chr6:13487750-13487760 chr6:13488144-13488158 chr6:13488515-13488524
28	POLR2A	chr6:13485896-13488307	GM19099	blood:	n/a	n/a
29	POLR2A	chr6:13487475-13488454	SK-N-MC	brain:	n/a	n/a
30	POLR2A	chr6:13486116-13488358	HL-60	blood:	n/a	n/a
31	POLR2A	chr6:13486622-13488336	MCF-7	breast:	n/a	n/a
32	MAZ	chr6:13487634-13488418	HepG2	liver:	n/a	n/a
33	POLR2A	chr6:13487392-13488400	MCF10A-Er-Src	breast:	n/a	n/a
34	ZNF263	chr6:13485651-13488433	HEK293-T-REx	kidney:	n/a	chr6:13486705-13486714
35	RUNX3	chr6:13488075-13488970	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:13487983-13488325	SK-N-SH	brain:	n/a	n/a
37	REST	chr6:13486305-13488706	H1-neurons	neurons:	n/a	chr6:13488639-13488646 chr6:13486435-13486448
38	POLR2A	chr6:13486140-13488291	GM15510	blood:	n/a	n/a
39	POLR2A	chr6:13487435-13488408	MCF10A-Er-Src	breast:	n/a	n/a
40	HA-E2F1	chr6:13486971-13488518	MCF-7	breast:	n/a	chr6:13487750-13487760 chr6:13488144-13488158
41	CEBPB	chr6:13488186-13488555	K562	blood:	n/a	n/a
42	E2F6	chr6:13487982-13489417	H1-hESC	embryonic stem cell:	n/a	chr6:13488882-13488892 chr6:13488624-13488633 chr6:13488144-13488158 chr6:13488515-13488524
43	POLR2A	chr6:13486177-13488411	H1-neurons	neurons:	n/a	n/a
44	CEBPB	chr6:13488214-13488567	HepG2	liver:	n/a	n/a
45	CEBPB	chr6:13488103-13488550	A549	lung:	n/a	n/a
46	POLR2A	chr6:13487243-13488598	HUVEC	blood vessel:	n/a	n/a
47	MAZ	chr6:13487625-13488474	GM12878	blood:	n/a	n/a
48	POLR2A	chr6:13486063-13488271	H1-neurons	neurons:	n/a	n/a
49	RAD21	chr6:13486957-13488263	H1-hESC	embryonic stem cell:	n/a	chr6:13487742-13487756
50	CEBPB	chr6:13488217-13488597	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:13328740..13330326-chr6:13487032..13488615,2	K562	blood:
2	chr6:13273285..13276286-chr6:13486162..13489029,3	K562	blood:
3	chr6:13408139..13410381-chr6:13486541..13489029,3	MCF-7	breast:
4	chr6:13273285..13276286-chr6:13486162..13489029,4	K562	blood:
5	chr6:13484664..13490672-chr6:13572714..13577234,9	K562	blood:
6	chr6:13484393..13490113-chr6:13572102..13578017,14	MCF-7	breast:
7	chr6:13465251..13472690-chr6:13481619..13489131,10	K562	blood:
8	chr6:13326316..13328538-chr6:13485562..13488530,2	MCF-7	breast:
9	chr6:13471062..13472931-chr6:13486374..13489089,2	MCF-7	breast:
10	chr6:13486147..13488786-chr6:13613803..13616517,3	K562	blood:
11	chr6:13485388..13489511-chr6:13572660..13577514,13	MCF-7	breast:
12	chr6:13325999..13330365-chr6:13484429..13488653,6	MCF-7	breast:
13	chr6:13488196..13489716-chr6:13537164..13538771,2	MCF-7	breast:
14	chr6:13486545..13489203-chr6:13612282..13616748,6	MCF-7	breast:
15	chr6:13486736..13489619-chr6:13614070..13616875,2	MCF-7	breast:

Variant related genes	Relation type
GFOD1	TF binding region
ENSG00000187461	TF binding region
ENSG00000261071	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000145979	Chromatin interaction
ENSG00000215022	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11759779	0.92[ASN][1000 genomes]
rs2115063	0.97[ASN][1000 genomes]
rs2841548	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841549	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7758810	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9367502	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370156	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382144	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382154	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9382156	0.80[EUR][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	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
7	esv3363743	chr6:13486598-13489146	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 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	chr6:13484200-13488600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:13484600-13488400	Active TSS	GM12878-XiMat	blood
4	chr6:13484800-13488400	Active TSS	Right Ventricle	heart
5	chr6:13485000-13488800	Active TSS	Brain Angular Gyrus	brain
6	chr6:13485000-13489600	Active TSS	Rectal Smooth Muscle	rectum
7	chr6:13485200-13488600	Active TSS	Left Ventricle	heart
8	chr6:13485200-13488600	Active TSS	A549	lung
9	chr6:13485200-13488800	Active TSS	Brain Anterior Caudate	brain
10	chr6:13485200-13488800	Active TSS	Psoas Muscle	Psoas
11	chr6:13485400-13488600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:13485400-13488600	Active TSS	NHDF-Ad	bronchial
13	chr6:13485600-13488600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr6:13485600-13488600	Active TSS	Esophagus	oesophagus
15	chr6:13485600-13488600	Active TSS	Lung	lung
16	chr6:13485600-13488800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr6:13485600-13488800	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr6:13485600-13489000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:13485800-13488600	Active TSS	Ovary	ovary
20	chr6:13486000-13488400	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr6:13486000-13488600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:13486000-13488600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:13486000-13488800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr6:13486000-13488800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:13486000-13488800	Active TSS	Aorta	Aorta
26	chr6:13486000-13488800	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr6:13486000-13489000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr6:13486000-13489000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
29	chr6:13486000-13489000	Active TSS	Fetal Brain Female	brain
30	chr6:13486000-13489000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr6:13486000-13489200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:13486200-13488400	Active TSS	HSMM	muscle
33	chr6:13486200-13488600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:13486200-13488800	Active TSS	Brain Cingulate Gyrus	brain
35	chr6:13486200-13488800	Active TSS	Brain Hippocampus Middle	brain
36	chr6:13486200-13488800	Active TSS	Brain Substantia Nigra	brain
37	chr6:13486200-13488800	Active TSS	NH-A	brain
38	chr6:13486200-13489000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:13486200-13489000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:13486200-13489000	Active TSS	Colon Smooth Muscle	Colon
41	chr6:13486200-13489200	Active TSS	NHEK	skin
42	chr6:13486400-13488600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
43	chr6:13486400-13488600	Active TSS	Fetal Kidney	kidney
44	chr6:13486400-13488800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:13486400-13488800	Active TSS	HUVEC	blood vessel
46	chr6:13486800-13488600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:13486800-13488600	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr6:13486800-13488800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr6:13486800-13488800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
50	chr6:13487000-13488600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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