Variant report

Variant	rs73407249
Chromosome Location	chr6:28831451-28831452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:313)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:313 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr6:28831225-28831777	A549	lung:	n/a	n/a
2	SIN3AK20	chr6:28831315-28831766	A549	lung:	n/a	n/a
3	MAFK	chr6:28831254-28831725	HepG2	liver:	n/a	n/a
4	RFX5	chr6:28831338-28831745	K562	blood:	n/a	n/a
5	MAX	chr6:28831121-28832395	MCF-7	breast:	n/a	n/a
6	TCF7L2	chr6:28830759-28832275	Hela-S3	cervix:	n/a	chr6:28831220-28831234 chr6:28831220-28831234
7	BATF	chr6:28831280-28831590	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr6:28831180-28832204	K562	blood:	n/a	n/a
9	BHLHE40	chr6:28831116-28831674	HepG2	liver:	n/a	n/a
10	MYC	chr6:28831127-28832221	K562	blood:	n/a	n/a
11	HDAC2	chr6:28831322-28832364	MCF-7	breast:	n/a	chr6:28831369-28831383
12	CEBPB	chr6:28831157-28831653	H1-hESC	embryonic stem cell:	n/a	chr6:28831410-28831421 chr6:28831410-28831421
13	TEAD4	chr6:28831335-28831791	A549	lung:	n/a	n/a
14	MAX	chr6:28831143-28832285	H1-hESC	embryonic stem cell:	n/a	n/a
15	GTF2F1	chr6:28831355-28832057	K562	blood:	n/a	n/a
16	YY1	chr6:28831071-28831579	K562	blood:	n/a	n/a
17	CEBPB	chr6:28831234-28831516	ECC-1	luminal epithelium:	n/a	chr6:28831410-28831421 chr6:28831410-28831421
18	YY1	chr6:28831124-28831606	K562	blood:	n/a	n/a
19	PAX5	chr6:28831248-28831700	GM12878	blood:	n/a	n/a
20	POU2F2	chr6:28831397-28831643	GM12878	blood:	n/a	n/a
21	TEAD4	chr6:28831162-28832317	ECC-1	luminal epithelium:	n/a	n/a
22	TCF7L2	chr6:28830437-28832244	HCT-116	colon:	n/a	chr6:28831220-28831234 chr6:28831220-28831234
23	EP300	chr6:28831266-28831657	GM12878	blood:	n/a	n/a
24	CEBPB	chr6:28831182-28831755	ECC-1	luminal epithelium:	n/a	chr6:28831410-28831421 chr6:28831410-28831421
25	FOXA2	chr6:28831305-28831621	HepG2	liver:	n/a	n/a
26	TBL1XR1	chr6:28831037-28832465	K562	blood:	n/a	n/a
27	MYC	chr6:28831415-28831639	Hela-S3	cervix:	n/a	n/a
28	MAX	chr6:28831209-28832185	A549	lung:	n/a	n/a
29	CBX3	chr6:28830979-28832539	HCT-116	colon:	n/a	n/a
30	JUND	chr6:28831203-28831756	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr6:28831352-28831649	A549	lung:	n/a	n/a
32	FOXA1	chr6:28831220-28831642	HepG2	liver:	n/a	n/a
33	MAX	chr6:28831216-28831729	SK-N-SH	brain:	n/a	n/a
34	TEAD4	chr6:28831148-28832355	SK-N-SH	brain:	n/a	n/a
35	GABPA	chr6:28831318-28831735	A549	lung:	n/a	n/a
36	CBX3	chr6:28829530-28832791	K562	blood:	n/a	n/a
37	MXI1	chr6:28831228-28832137	HepG2	liver:	n/a	n/a
38	MAX	chr6:28831218-28832362	SK-N-SH	brain:	n/a	n/a
39	JUND	chr6:28831307-28831700	A549	lung:	n/a	n/a
40	MBD4	chr6:28831075-28831743	HepG2	liver:	n/a	n/a
41	ATF3	chr6:28831036-28831835	K562	blood:	n/a	n/a
42	ZEB1	chr6:28831211-28832405	HepG2	liver:	n/a	n/a
43	STAT3	chr6:28831400-28831714	MCF10A-Er-Src	breast:	n/a	n/a
44	USF1	chr6:28831317-28831649	A549	lung:	n/a	n/a
45	GABPA	chr6:28831345-28831654	Hela-S3	cervix:	n/a	n/a
46	MYBL2	chr6:28831129-28832320	HepG2	liver:	n/a	n/a
47	MXI1	chr6:28831189-28831702	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr6:28831213-28831773	PANC-1	pancreas:	n/a	n/a
49	ETS1	chr6:28831190-28831778	K562	blood:	n/a	n/a
50	BDP1	chr6:28831341-28831902	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28803282..28808663-chr6:28829877..28836776,13	K562	blood:
2	chr6:27859769..27862740-chr6:28829876..28831991,2	K562	blood:
3	chr6:28803282..28808495-chr6:28830531..28834946,8	K562	blood:
4	chr6:28830168..28831847-chr6:28972589..28974401,2	K562	blood:
5	chr6:28828478..28839935-chr6:28855092..28866386,31	K562	blood:
6	chr6:28830882..28836292-chr6:28860588..28866545,10	MCF-7	breast:
7	chr6:28830568..28832864-chr6:28971652..28974126,2	K562	blood:
8	chr6:28831130..28836886-chr6:28890033..28892870,9	MCF-7	breast:
9	chr6:28823126..28835109-chr6:28859268..28867076,23	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM27-3	chr6:28831061-28831454	ENSG00000225595.2
2	lnc-TRIM27-3	chr6:28831061-28831454	NONHSAT108488

No data

Variant related genes	Relation type
ENSG00000225595	TF binding region
ENSG00000233224	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000225173	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1925764	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6929090	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935576	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73403168	0.86[EUR][1000 genomes]
rs73403188	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73407250	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7739709	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7762991	0.83[ASN][1000 genomes]
rs7763504	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468430	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9501112	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9501420	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][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	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
4	esv3403240	chr6:28808022-28832799	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28830400-28832200	Active TSS	Hela-S3	cervix
2	chr6:28830400-28833000	Active TSS	Fetal Brain Female	brain
3	chr6:28830600-28832200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:28830600-28832200	Active TSS	Brain Anterior Caudate	brain
5	chr6:28830600-28832200	Active TSS	Brain Cingulate Gyrus	brain
6	chr6:28830600-28834800	Active TSS	A549	lung
7	chr6:28830800-28832200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:28830800-28832200	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:28830800-28832200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
10	chr6:28830800-28832200	Active TSS	Brain Substantia Nigra	brain
11	chr6:28830800-28832400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:28830800-28832400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr6:28830800-28832400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr6:28830800-28832400	Active TSS	Fetal Brain Male	brain
15	chr6:28830800-28832600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr6:28830800-28832600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr6:28831000-28831600	Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr6:28831000-28832000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:28831000-28832000	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr6:28831000-28832000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:28831000-28832000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr6:28831000-28832000	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr6:28831000-28832200	Active TSS	H1 Cell Line	embryonic stem cell
24	chr6:28831000-28832200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:28831000-28832200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:28831000-28832200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:28831000-28832200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:28831000-28832200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:28831000-28832200	Active TSS	Brain Hippocampus Middle	brain
30	chr6:28831000-28832200	Active TSS	Duodenum Mucosa	Duodenum
31	chr6:28831000-28832200	Active TSS	HSMM	muscle
32	chr6:28831000-28832200	Active TSS	NHLF	lung
33	chr6:28831000-28832400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:28831000-28832400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:28831000-28832400	Active TSS	HSMMtube	muscle
36	chr6:28831000-28832600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:28831000-28832600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr6:28831000-28832600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:28831000-28832600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr6:28831000-28834800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:28831000-28835000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:28831200-28831600	Active TSS	Primary hematopoietic stem cells	blood
43	chr6:28831200-28831600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:28831200-28831600	Enhancers	Fetal Heart	heart
45	chr6:28831200-28831600	Enhancers	Gastric	stomach
46	chr6:28831200-28831600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr6:28831200-28831800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:28831200-28831800	Active TSS	Adipose Nuclei	Adipose
49	chr6:28831200-28831800	Active TSS	Fetal Muscle Trunk	muscle
50	chr6:28831200-28832000	Active TSS	NH-A	brain

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