Variant report

Variant	rs73779539
Chromosome Location	chr6:149970085-149970086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:284)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:284 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:149969329-149970141	MCF-7	breast:	n/a	n/a
2	CTCF	chr6:149970020-149970170	SK-N-SH_RA	brain:	n/a	n/a
3	CTCF	chr6:149970000-149970150	HEK293	kidney:	n/a	n/a
4	POLR2A	chr6:149968338-149970211	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr6:149969450-149970125	GM12892	blood:	n/a	n/a
6	E2F6	chr6:149969326-149970140	K562	blood:	n/a	chr6:149969887-149969898
7	GTF2B	chr6:149969527-149970155	K562	blood:	n/a	n/a
8	POLR2A	chr6:149969383-149970245	GM12892	blood:	n/a	n/a
9	POLR2A	chr6:149969491-149970254	U87	brain:	n/a	n/a
10	MTA3	chr6:149969385-149970355	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:149969635-149970112	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr6:149969434-149970152	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr6:149969520-149970094	HepG2	liver:	n/a	n/a
14	NRF1	chr6:149969816-149970118	HepG2	liver:	n/a	chr6:149969928-149969939
15	ZNF143	chr6:149969680-149970120	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:149969280-149970731	HepG2	liver:	n/a	n/a
17	YY1	chr6:149969343-149970086	K562	blood:	n/a	n/a
18	RCOR1	chr6:149969545-149970228	HepG2	liver:	n/a	n/a
19	IRF1	chr6:149969423-149970175	K562	blood:	n/a	n/a
20	MYBL2	chr6:149969446-149970331	HepG2	liver:	n/a	n/a
21	MYC	chr6:149969596-149970152	K562	blood:	n/a	n/a
22	POLR2A	chr6:149969535-149970141	A549	lung:	n/a	n/a
23	ATF2	chr6:149969710-149970233	GM12878	blood:	n/a	n/a
24	RUNX3	chr6:149969462-149970137	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:149969443-149970134	GM12892	blood:	n/a	n/a
26	POLR2A	chr6:149969515-149970112	HepG2	liver:	n/a	n/a
27	ZMIZ1	chr6:149969506-149970148	K562	blood:	n/a	n/a
28	BACH1	chr6:149969659-149970209	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr6:149969165-149970226	K562	blood:	n/a	n/a
30	KAP1	chr6:149969525-149970319	K562	blood:	n/a	n/a
31	NFIC	chr6:149969438-149970269	HepG2	liver:	n/a	n/a
32	STAT5A	chr6:149969507-149970240	K562	blood:	n/a	n/a
33	REST	chr6:149969279-149970568	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr6:149969525-149970183	HepG2	liver:	n/a	n/a
35	CHD2	chr6:149969447-149970117	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr6:149969153-149970452	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr6:149969375-149970208	ProgFib	skin:	n/a	n/a
38	SP4	chr6:149969631-149970117	H1-hESC	embryonic stem cell:	n/a	n/a
39	ATF2	chr6:149969592-149970147	GM12878	blood:	n/a	n/a
40	HCFC1	chr6:149969146-149970333	Hela-S3	cervix:	n/a	n/a
41	NRF1	chr6:149969606-149970137	GM12878	blood:	n/a	chr6:149969928-149969939
42	POLR2A	chr6:149969470-149970156	GM12878	blood:	n/a	n/a
43	ELF1	chr6:149969453-149970172	MCF-7	breast:	n/a	chr6:149969816-149969829
44	HEY1	chr6:149969905-149970126	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:149969327-149970189	MCF10A-Er-Src	breast:	n/a	n/a
46	USF2	chr6:149969616-149970162	HepG2	liver:	n/a	n/a
47	POLR2A	chr6:149969384-149970293	PFSK-1	brain:	n/a	n/a
48	ZNF263	chr6:149969248-149970584	HEK293-T-REx	kidney:	n/a	chr6:149969951-149969960 chr6:149970223-149970232
49	HEY1	chr6:149969383-149970266	HepG2	liver:	n/a	n/a
50	YY1	chr6:149969614-149970183	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149967586..149970977-chr6:150068764..150072371,6	K562	blood:
2	chr6:149884132..149889842-chr6:149966518..149971305,10	K562	blood:
3	chr6:149967293..149971613-chr6:150037790..150041524,8	K562	blood:
4	chr6:149864361..149868960-chr6:149967728..149970352,9	K562	blood:
5	chr6:149865149..149869984-chr6:149967517..149970273,6	K562	blood:
6	chr6:149966676..149970226-chr6:150037413..150039390,4	MCF-7	breast:
7	chr6:149968177..149971048-chr6:150069429..150073118,6	K562	blood:
8	chr6:149967309..149971944-chr6:150037502..150040952,6	MCF-7	breast:
9	chr6:149969487..149971965-chr6:150038903..150040820,3	K562	blood:
10	chr6:149884836..149889436-chr6:149966369..149971850,7	K562	blood:

No data

Variant related genes	Relation type
KATNA1	TF binding region
ENSG00000120265	Chromatin interaction
ENSG00000055211	Chromatin interaction
ENSG00000120253	Chromatin interaction
ENSG00000131013	Chromatin interaction
ENSG00000131023	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs55810699	0.93[AFR][1000 genomes]
rs55858131	0.81[AFR][1000 genomes]
rs59865840	0.81[AFR][1000 genomes]
rs73779541	1.00[AFR][1000 genomes]
rs73779544	0.93[AFR][1000 genomes]
rs73779546	0.81[AFR][1000 genomes]
rs73779552	1.00[AFR][1000 genomes]
rs73779581	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv289	chr6:149864898-149998818	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv5534	chr6:149864898-149998818	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1792620	chr6:149909491-150083621	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 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	chr6:149967600-149970400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:149967600-149970400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:149967600-149970400	Active TSS	NHLF	lung
4	chr6:149967800-149970200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:149967800-149970200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:149967800-149970400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:149967800-149970400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:149967800-149970400	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:149967800-149970400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:149967800-149970400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:149967800-149970400	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr6:149967800-149970800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:149968000-149970200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:149968000-149970200	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr6:149968000-149970200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:149968000-149970400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr6:149968000-149970400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:149968000-149970400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr6:149968000-149970400	Active TSS	Psoas Muscle	Psoas
20	chr6:149968000-149970400	Active TSS	Right Ventricle	heart
21	chr6:149968000-149970400	Active TSS	HSMM	muscle
22	chr6:149968000-149970600	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr6:149968200-149970200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:149968200-149970200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:149968200-149970200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr6:149968200-149970200	Active TSS	Duodenum Mucosa	Duodenum
27	chr6:149968200-149970200	Active TSS	Fetal Intestine Large	intestine
28	chr6:149968200-149970200	Active TSS	NHDF-Ad	bronchial
29	chr6:149968200-149970400	Active TSS	H9 Cell Line	embryonic stem cell
30	chr6:149968200-149970400	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr6:149968200-149970400	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr6:149968200-149970400	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr6:149968200-149970400	Active TSS	Muscle Satellite Cultured Cells	--
34	chr6:149968200-149970400	Active TSS	HSMMtube	muscle
35	chr6:149968200-149970600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:149968200-149970600	Active TSS	Rectal Smooth Muscle	rectum
37	chr6:149968400-149970200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:149968400-149970200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:149968400-149970200	Active TSS	Brain Substantia Nigra	brain
40	chr6:149968400-149970200	Active TSS	Esophagus	oesophagus
41	chr6:149968400-149970200	Active TSS	Placenta	Placenta
42	chr6:149968400-149970200	Active TSS	Pancreas	Pancrea
43	chr6:149968400-149970400	Active TSS	Brain Angular Gyrus	brain
44	chr6:149968400-149970400	Active TSS	Brain Hippocampus Middle	brain
45	chr6:149968400-149970400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:149968400-149970400	Active TSS	Colonic Mucosa	Colon
47	chr6:149968400-149970600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:149968400-149970600	Active TSS	Stomach Smooth Muscle	stomach
49	chr6:149968600-149970200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:149968600-149970200	Active TSS	Cortex derived primary cultured neurospheres	brain

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