Variant report

Variant	rs1746479
Chromosome Location	chr6:131457295-131457296
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	RAD21	chr6:131457272-131457505	HepG2	liver:	n/a	n/a
2	TBP	chr6:131457040-131457526	Hela-S3	cervix:	n/a	n/a
3	MAX	chr6:131456030-131457706	HepG2	liver:	n/a	chr6:131456304-131456314 chr6:131456533-131456543 chr6:131456434-131456444 chr6:131456378-131456388
4	ZKSCAN1	chr6:131456226-131457534	Hela-S3	cervix:	n/a	n/a
5	SIN3AK20	chr6:131457046-131457493	HepG2	liver:	n/a	n/a
6	HNF4A	chr6:131456289-131457622	HepG2	liver:	n/a	chr6:131457207-131457219 chr6:131457455-131457463 chr6:131457219-131457231 chr6:131457217-131457232 chr6:131457219-131457231 chr6:131457484-131457492
7	POLR2A	chr6:131455747-131457842	MCF10A-Er-Src	breast:	n/a	n/a
8	SRF	chr6:131457284-131457610	HepG2	liver:	n/a	n/a
9	RFX5	chr6:131457065-131457509	HepG2	liver:	n/a	n/a
10	YY1	chr6:131457145-131457506	HepG2	liver:	n/a	n/a
11	CTCF	chr6:131457160-131457310	HMF	breast:	n/a	n/a
12	CREB1	chr6:131456214-131457650	HepG2	liver:	n/a	n/a
13	RCOR1	chr6:131456328-131457473	HepG2	liver:	n/a	n/a
14	MYC	chr6:131457017-131457968	MCF10A-Er-Src	breast:	n/a	n/a
15	MBD4	chr6:131456970-131457636	HepG2	liver:	n/a	n/a
16	UBTF	chr6:131456334-131457653	K562	blood:	n/a	n/a
17	MAFK	chr6:131457179-131457671	HepG2	liver:	n/a	n/a
18	HDAC2	chr6:131456196-131457602	HepG2	liver:	n/a	chr6:131457186-131457200
19	POLR2A	chr6:131455744-131457623	HepG2	liver:	n/a	n/a
20	MYC	chr6:131456149-131457326	K562	blood:	n/a	chr6:131456304-131456314 chr6:131456533-131456543 chr6:131456434-131456444 chr6:131456378-131456388
21	MYC	chr6:131456009-131457421	MCF10A-Er-Src	breast:	n/a	chr6:131456304-131456314 chr6:131456533-131456543 chr6:131456434-131456444 chr6:131456378-131456388
22	POLR2A	chr6:131456460-131457426	K562	blood:	n/a	n/a
23	MYC	chr6:131456120-131457336	A549	lung:	n/a	chr6:131456304-131456314 chr6:131456533-131456543 chr6:131456434-131456444 chr6:131456378-131456388
24	FOXA1	chr6:131456977-131457652	HepG2	liver:	n/a	n/a
25	SIN3AK20	chr6:131456298-131457341	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr6:131456248-131457507	HepG2	liver:	n/a	n/a
27	HNF4A	chr6:131457045-131457639	HepG2	liver:	n/a	chr6:131457207-131457219 chr6:131457455-131457463 chr6:131457219-131457231 chr6:131457217-131457232 chr6:131457219-131457231 chr6:131457484-131457492
28	POLR2A	chr6:131456863-131457605	SK-N-MC	brain:	n/a	n/a
29	MAFK	chr6:131457060-131457777	HepG2	liver:	n/a	n/a
30	MAZ	chr6:131456318-131457518	HepG2	liver:	n/a	chr6:131456533-131456543 chr6:131456434-131456444 chr6:131456378-131456388
31	HA-E2F1	chr6:131456252-131457672	MCF-7	breast:	n/a	chr6:131457151-131457160 chr6:131457016-131457025 chr6:131457391-131457402 chr6:131457388-131457405
32	ARID3A	chr6:131457111-131457634	HepG2	liver:	n/a	n/a
33	MAX	chr6:131456285-131457412	HepG2	liver:	n/a	chr6:131456304-131456314 chr6:131456533-131456543 chr6:131456434-131456444 chr6:131456378-131456388
34	POLR2A	chr6:131457244-131457312	GM12878	blood:	n/a	n/a
35	SMC3	chr6:131456941-131457309	Hela-S3	cervix:	n/a	n/a
36	SIN3AK20	chr6:131457153-131457534	HepG2	liver:	n/a	n/a
37	E2F4	chr6:131457005-131457971	MCF10A-Er-Src	breast:	n/a	chr6:131457151-131457160 chr6:131457016-131457025 chr6:131457391-131457402 chr6:131457388-131457405
38	HEY1	chr6:131456201-131457666	HepG2	liver:	n/a	chr6:131456942-131456957
39	MAFK	chr6:131457178-131457460	Hela-S3	cervix:	n/a	n/a
40	CTCF	chr6:131457260-131457410	AG10803	skin:	n/a	n/a
41	POLR2A	chr6:131456274-131457530	HepG2	liver:	n/a	n/a
42	CTCF	chr6:131457200-131457350	HAc	cerebellar:	n/a	n/a
43	MAX	chr6:131456264-131457459	K562	blood:	n/a	chr6:131456304-131456314 chr6:131456533-131456543 chr6:131456434-131456444 chr6:131456378-131456388
44	FOXA2	chr6:131457103-131457400	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:131456270-131457327	PFSK-1	brain:	n/a	n/a
46	MAX	chr6:131456090-131457613	HepG2	liver:	n/a	chr6:131456304-131456314 chr6:131456533-131456543 chr6:131456434-131456444 chr6:131456378-131456388
47	TBP	chr6:131456144-131457697	HepG2	liver:	n/a	n/a
48	HEY1	chr6:131456199-131457520	HepG2	liver:	n/a	chr6:131456942-131456957
49	POLR2A	chr6:131456285-131457302	GM19099	blood:	n/a	n/a
50	JUND	chr6:131456973-131457325	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131456917..131458462-chr6:131459846..131461723,2	MCF-7	breast:

Variant related genes	Relation type
AKAP7	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs478984	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs543363	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs629208	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs645550	0.85[EUR][1000 genomes]
rs663982	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs674337	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs677072	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	esv3398888	chr6:131455859-131457857	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131455600-131458000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr6:131455600-131458200	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:131455800-131457400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:131455800-131457400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr6:131455800-131457600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:131455800-131457600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:131455800-131457600	Active TSS	Brain Angular Gyrus	brain
8	chr6:131455800-131457600	Active TSS	NH-A	brain
9	chr6:131455800-131457800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr6:131455800-131457800	Active TSS	Psoas Muscle	Psoas
11	chr6:131455800-131457800	Active TSS	HSMM	muscle
12	chr6:131455800-131458000	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:131456000-131457400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:131456000-131457400	Active TSS	Fetal Stomach	stomach
15	chr6:131456000-131457600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:131456000-131457600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:131456000-131457600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:131456000-131457600	Active TSS	Brain Anterior Caudate	brain
19	chr6:131456000-131457600	Active TSS	Brain Cingulate Gyrus	brain
20	chr6:131456000-131457600	Active TSS	Brain Substantia Nigra	brain
21	chr6:131456000-131457600	Active TSS	Colonic Mucosa	Colon
22	chr6:131456000-131457600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr6:131456000-131457600	Active TSS	Fetal Brain Female	brain
24	chr6:131456000-131457600	Active TSS	Osteobl	bone
25	chr6:131456000-131457800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:131456000-131457800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:131456000-131457800	Active TSS	Brain Hippocampus Middle	brain
28	chr6:131456000-131457800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:131456000-131457800	Active TSS	Fetal Lung	lung
30	chr6:131456000-131457800	Active TSS	Ovary	ovary
31	chr6:131456000-131458000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr6:131456000-131458000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:131456000-131458000	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr6:131456000-131458000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:131456000-131458000	Active TSS	Fetal Muscle Leg	muscle
36	chr6:131456000-131458000	Active TSS	Right Atrium	heart
37	chr6:131456000-131458200	Active TSS	NHDF-Ad	bronchial
38	chr6:131456200-131457400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:131456200-131457400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:131456200-131457400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:131456200-131457400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:131456200-131457400	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr6:131456200-131457400	Active TSS	Gastric	stomach
44	chr6:131456200-131457400	Active TSS	Placenta Amnion	Placenta Amnion
45	chr6:131456200-131457400	Active TSS	Rectal Smooth Muscle	rectum
46	chr6:131456200-131457400	Active TSS	Dnd41	blood
47	chr6:131456200-131457600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:131456200-131457600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr6:131456200-131457600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:131456200-131457600	Active TSS	Esophagus	oesophagus

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