Variant report

Variant	rs28780113
Chromosome Location	chr6:30749301-30749302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:106)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:106 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr6:30749179-30750877	A549	lung:	n/a	chr6:30749928-30749942
2	MAFK	chr6:30749282-30750413	K562	blood:	n/a	n/a
3	CEBPB	chr6:30749245-30750831	A549	lung:	n/a	chr6:30750630-30750641 chr6:30749779-30749790
4	TCF12	chr6:30749069-30751165	A549	lung:	n/a	n/a
5	BCL3	chr6:30749287-30750863	A549	lung:	n/a	chr6:30749933-30749942
6	TCF7L2	chr6:30749293-30750024	Hela-S3	cervix:	n/a	n/a
7	RCOR1	chr6:30749243-30750915	Hela-S3	cervix:	n/a	n/a
8	SP1	chr6:30749163-30751008	A549	lung:	n/a	n/a
9	TBL1XR1	chr6:30749283-30750277	K562	blood:	n/a	n/a
10	POLR2A	chr6:30749027-30751412	Hela-S3	cervix:	n/a	n/a
11	JUND	chr6:30749212-30750239	SK-N-SH	brain:	n/a	n/a
12	USF2	chr6:30749220-30749969	Hela-S3	cervix:	n/a	n/a
13	MAFK	chr6:30749212-30750166	IMR90	lung:	n/a	n/a
14	POLR2A	chr6:30748460-30750969	Hela-S3	cervix:	n/a	n/a
15	TBP	chr6:30749296-30750884	Hela-S3	cervix:	n/a	n/a
16	EP300	chr6:30749147-30750727	SK-N-SH	brain:	n/a	chr6:30749928-30749942
17	JUN	chr6:30749176-30750932	K562	blood:	n/a	chr6:30750238-30750245 chr6:30749810-30749823
18	SMARCC1	chr6:30749148-30750479	Hela-S3	cervix:	n/a	n/a
19	NFIC	chr6:30749234-30750853	ECC-1	luminal epithelium:	n/a	n/a
20	STAT3	chr6:30749294-30750761	Hela-S3	cervix:	n/a	n/a
21	GTF2F1	chr6:30749249-30750724	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr6:30749070-30750972	HCT-116	colon:	n/a	chr6:30750630-30750641 chr6:30749779-30749790
23	GATA3	chr6:30749169-30750720	SK-N-SH	brain:	n/a	chr6:30749943-30749950
24	MAX	chr6:30749259-30750904	A549	lung:	n/a	n/a
25	JUND	chr6:30749247-30750738	K562	blood:	n/a	chr6:30750238-30750245
26	POLR2A	chr6:30749174-30750113	HL-60	blood:	n/a	n/a
27	JUND	chr6:30749079-30750410	SK-N-SH	brain:	n/a	chr6:30750238-30750245
28	MAX	chr6:30749125-30750937	HepG2	liver:	n/a	n/a
29	SP1	chr6:30749180-30750966	HCT-116	colon:	n/a	n/a
30	GATA3	chr6:30749063-30750982	A549	lung:	n/a	chr6:30749943-30749950
31	FOS	chr6:30749258-30750039	MCF10A-Er-Src	breast:	n/a	n/a
32	SMC3	chr6:30749205-30750786	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr6:30749253-30750082	Hela-S3	cervix:	n/a	n/a
34	CHD1	chr6:30746278-30750816	IMR90	lung:	n/a	n/a
35	FOSL1	chr6:30749151-30750847	HCT-116	colon:	n/a	chr6:30750238-30750245
36	RAD21	chr6:30749220-30750790	Hela-S3	cervix:	n/a	n/a
37	GATA3	chr6:30749294-30750287	SK-N-SH	brain:	n/a	chr6:30749943-30749950
38	FOS	chr6:30749271-30750066	MCF10A-Er-Src	breast:	n/a	n/a
39	CEBPB	chr6:30749272-30750831	K562	blood:	n/a	chr6:30750630-30750641 chr6:30749779-30749790
40	RXRA	chr6:30749211-30750234	SK-N-SH	brain:	n/a	chr6:30749933-30749942 chr6:30749672-30749691
41	TAF1	chr6:30749187-30750103	Hela-S3	cervix:	n/a	n/a
42	BRCA1	chr6:30749278-30750153	Hela-S3	cervix:	n/a	n/a
43	CEBPB	chr6:30749160-30750886	A549	lung:	n/a	chr6:30750630-30750641 chr6:30749779-30749790
44	MAFK	chr6:30749166-30750652	Hela-S3	cervix:	n/a	n/a
45	FOS	chr6:30749273-30750744	MCF10A-Er-Src	breast:	n/a	chr6:30750238-30750245
46	E2F6	chr6:30749194-30750022	A549	lung:	n/a	n/a
47	SP1	chr6:30749144-30750914	HCT-116	colon:	n/a	n/a
48	FOS	chr6:30749280-30749988	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr6:30749223-30749668	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr6:30749145-30750035	U87	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30749279-30749329	IMR90	lung:	fetal
2	chr6:30749279-30749329	BJ	skin:	n/a
3	chr6:30749279-30749329	HCPEpiC	choroid plexus:	n/a
4	chr6:30749279-30749329	Hepatocyte	liver:	n/a
5	chr6:30749279-30749329	AoSMC	blood vessel:	n/a
6	chr6:30749279-30749329	HAEpiC	amniotic membrane:	n/a
7	chr6:30749279-30749329	HCM	heart:	n/a
8	chr6:30749279-30749329	NB4	blood:	n/a
9	chr6:30749279-30749329	PANC-1	pancreas:	n/a
10	chr6:30749279-30749329	HUVEC	blood vessel:	n/a
11	chr6:30749279-30749329	ECC-1	luminal epithelium:	n/a
12	chr6:30749279-30749329	MCF10A-Er-Src	breast:	n/a
13	chr6:30749279-30749329	PrEC	prostate:	n/a
14	chr6:30749279-30749329	HCT-116	colon:	n/a
15	chr6:30749279-30749329	NHDF-neo	bronchial:	n/a
16	chr6:30749279-30749329	HRPEpiC	eye:	n/a
17	chr6:30749279-30749329	NHBE	bronchial:	n/a
18	chr6:30749279-30749329	NT2-D1	testis:	n/a
19	chr6:30749279-30749329	H1-hESC	embryonic stem cell:	embryo
20	chr6:30749279-30749329	HCF	heart:	n/a
21	chr6:30749279-30749329	HRCEpiC	kidney:	n/a
22	chr6:30749279-30749329	HPAEpiC	pulmonary alveolar:	n/a
23	chr6:30749279-30749329	ProgFib	skin:	n/a
24	chr6:30749279-30749329	HEEpiC	esophagus:	n/a
25	chr6:30749279-30749329	HepG2	liver:	n/a
26	chr6:30749279-30749329	HIPEpiC	eye:	n/a
27	chr6:30749279-30749329	AG04450	lung:	fetal
28	chr6:30749279-30749329	HRE	kidney:	n/a
29	chr6:30749279-30749329	ovcar-3	ovarian:	n/a
30	chr6:30749279-30749329	AG10803	skin:	n/a
31	chr6:30749279-30749329	A549	lung:	n/a
32	chr6:30749279-30749329	NH-A	brain:	n/a
33	chr6:30749279-30749329	GM06990	blood:	n/a
34	chr6:30749279-30749329	SK-N-SH_RA	brain:	n/a
35	chr6:30749279-30749329	AG04449	skin:	fetal
36	chr6:30749279-30749329	BE2_C	brain:	n/a
37	chr6:30749279-30749329	GM12892	blood:	n/a
38	chr6:30749279-30749329	AG09309	skin:	n/a
39	chr6:30749279-30749329	SKMC	muscle:	n/a
40	chr6:30749279-30749329	PFSK-1	brain:	n/a
41	chr6:30749279-30749329	HNPCEpiC	eye:	n/a
42	chr6:30749279-30749329	Jurkat	blood:	n/a
43	chr6:30749279-30749329	SK-N-MC	brain:	n/a
44	chr6:30749279-30749329	HL-60	blood:	n/a
45	chr6:30749279-30749329	GM19239	blood:	n/a
46	chr6:30749279-30749329	SAEC	small airway:	n/a
47	chr6:30749279-30749329	GM12878	blood:	n/a
48	chr6:30749279-30749329	U87	brain:	n/a
49	chr6:30749279-30749329	AG09319	gingival:	n/a
50	chr6:30749279-30749329	Hela-S3	cervix:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr6:30583409..30587215-chr6:30748473..30750740,4	K562	blood:
2	chr6:30657201..30658778-chr6:30748296..30750541,2	K562	blood:
3	chr6:30748758..30751430-chr6:30850690..30852588,5	MCF-7	breast:
4	chr6:30613838..30616795-chr6:30748344..30751338,2	K562	blood:
5	chr6:30748393..30749996-chr6:30841265..30843895,2	K562	blood:
6	chr6:30747932..30749847-chr6:30861062..30862984,2	K562	blood:
7	chr6:30685130..30687169-chr6:30748703..30751412,3	K562	blood:
8	chr15:64994923..64995558-chr6:30748917..30749642,2	Hela-S3	cervix:
9	chr6:27100755..27102737-chr6:30749085..30751315,2	K562	blood:
10	chr6:30710424..30713995-chr6:30746295..30752430,9	K562	blood:

No data

Variant related genes	Relation type
HCG20	TF binding region
HCG20	CpG island
ENSG00000272273	Chromatin interaction
ENSG00000137404	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000180304	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000204568	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12526186	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12527188	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12660860	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12660883	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12662149	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13202739	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13214831	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13217914	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13220225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189441	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17481190	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28670020	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28780111	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28780114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28780120	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28780121	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28780122	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28894082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3869075	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4278006	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713361	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
10	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv884104	chr6:30740680-30753146	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30741000-30749600	Weak transcription	Thymus	Thymus
2	chr6:30744000-30758000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:30744800-30749400	Enhancers	Stomach Mucosa	stomach
4	chr6:30745400-30749600	Enhancers	Fetal Muscle Leg	muscle
5	chr6:30745600-30749400	Enhancers	Fetal Muscle Trunk	muscle
6	chr6:30746000-30749400	Enhancers	Lung	lung
7	chr6:30746000-30749800	Enhancers	Pancreas	Pancrea
8	chr6:30746000-30750000	Enhancers	Left Ventricle	heart
9	chr6:30746000-30750400	Enhancers	Fetal Stomach	stomach
10	chr6:30746000-30750400	Enhancers	Spleen	Spleen
11	chr6:30746000-30750800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:30746000-30750800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr6:30746000-30751000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr6:30746000-30752400	Enhancers	Placenta	Placenta
15	chr6:30746200-30749400	Weak transcription	Dnd41	blood
16	chr6:30746200-30751400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:30746600-30749400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr6:30746600-30750400	Enhancers	Aorta	Aorta
19	chr6:30746600-30751000	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:30746800-30751200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:30747000-30750600	Enhancers	HUVEC	blood vessel
22	chr6:30747000-30751400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:30747200-30749400	Enhancers	Gastric	stomach
24	chr6:30747200-30751000	Enhancers	Right Ventricle	heart
25	chr6:30747400-30749400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr6:30747400-30750600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr6:30747400-30751000	Enhancers	NHLF	lung
28	chr6:30747600-30749400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:30747600-30749400	Enhancers	Duodenum Mucosa	Duodenum
30	chr6:30747600-30750000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:30747600-30750000	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr6:30747600-30750000	Enhancers	HMEC	breast
33	chr6:30747800-30749400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:30747800-30749800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:30748000-30749600	Weak transcription	Esophagus	oesophagus
36	chr6:30748200-30750600	Enhancers	Primary hematopoietic stem cells	blood
37	chr6:30748200-30751400	Enhancers	Liver	Liver
38	chr6:30748200-30753800	Weak transcription	Primary T cells from cord blood	blood
39	chr6:30748600-30750000	Enhancers	Psoas Muscle	Psoas
40	chr6:30748600-30750800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr6:30748800-30749800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:30748800-30749800	Enhancers	Ovary	ovary
43	chr6:30748800-30750000	Flanking Active TSS	Stomach Smooth Muscle	stomach
44	chr6:30748800-30750200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:30748800-30751000	Enhancers	Primary B cells from cord blood	blood
46	chr6:30748800-30751400	Enhancers	Fetal Intestine Small	intestine
47	chr6:30748800-30751400	Flanking Active TSS	Hela-S3	cervix
48	chr6:30749000-30749400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:30749000-30749400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:30749000-30749600	Flanking Active TSS	Brain Germinal Matrix	brain

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