Variant report

Variant	rs541211853
Chromosome Location	chr6:30059892-30059893
allele	A/C
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	MAX	chr6:30059289-30060018	MCF-7	breast:	n/a	chr6:30059640-30059650
2	TCF7L2	chr6:30059493-30060119	HCT-116	colon:	n/a	n/a
3	MAX	chr6:30058912-30060334	HCT-116	colon:	n/a	chr6:30059640-30059650
4	NFIC	chr6:30059477-30059982	ECC-1	luminal epithelium:	n/a	n/a
5	E2F6	chr6:30059358-30059922	Hela-S3	cervix:	n/a	n/a
6	ZKSCAN1	chr6:30059414-30059928	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr6:30059718-30060285	SK-N-MC	brain:	n/a	n/a
8	YY1	chr6:30059828-30060152	HCT-116	colon:	n/a	chr6:30060033-30060044
9	RCOR1	chr6:30059461-30059911	Hela-S3	cervix:	n/a	n/a
10	MAFK	chr6:30059603-30059944	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr6:30059314-30060334	HCT-116	colon:	n/a	n/a
12	E2F6	chr6:30059270-30059989	H1-hESC	embryonic stem cell:	n/a	n/a
13	SMARCC1	chr6:30059454-30060020	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr6:30059277-30060217	U87	brain:	n/a	n/a
15	GTF2F1	chr6:30059465-30059909	Hela-S3	cervix:	n/a	n/a
16	MXI1	chr6:30059361-30059946	IMR90	lung:	n/a	n/a
17	TCF7L2	chr6:30059420-30060091	Hela-S3	cervix:	n/a	n/a
18	NFYA	chr6:30059508-30060126	Hela-S3	cervix:	n/a	n/a
19	YY1	chr6:30059676-30060122	HepG2	liver:	n/a	chr6:30060033-30060044
20	POLR2A	chr6:30059277-30060197	U87	brain:	n/a	n/a
21	POLR2A	chr6:30059286-30060011	U87	brain:	n/a	n/a
22	MAX	chr6:30059395-30059953	ECC-1	luminal epithelium:	n/a	chr6:30059640-30059650
23	POLR2A	chr6:30059391-30060109	Hela-S3	cervix:	n/a	n/a
24	E2F6	chr6:30059370-30059947	A549	lung:	n/a	n/a
25	MAX	chr6:30059302-30059957	A549	lung:	n/a	chr6:30059640-30059650
26	MAX	chr6:30059288-30060179	ECC-1	luminal epithelium:	n/a	chr6:30059640-30059650
27	MAX	chr6:30059424-30059916	Hela-S3	cervix:	n/a	chr6:30059640-30059650
28	MAZ	chr6:30059457-30059919	Hela-S3	cervix:	n/a	n/a
29	CBX3	chr6:30059166-30060383	HCT-116	colon:	n/a	n/a
30	MAX	chr6:30059482-30059893	H1-hESC	embryonic stem cell:	n/a	chr6:30059640-30059650
31	MAX	chr6:30059298-30059996	HepG2	liver:	n/a	chr6:30059640-30059650
32	MAX	chr6:30059328-30059959	MCF-7	breast:	n/a	chr6:30059640-30059650
33	POLR2A	chr6:30059386-30060112	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr6:30059397-30060221	HCT-116	colon:	n/a	n/a
35	MAX	chr6:30059111-30060374	HCT-116	colon:	n/a	chr6:30059640-30059650
36	MYC	chr6:30059374-30059915	MCF10A-Er-Src	breast:	n/a	chr6:30059640-30059650
37	POLR2A	chr6:30059853-30059927	MCF-7	breast:	n/a	n/a
38	MAX	chr6:30059404-30060112	Hela-S3	cervix:	n/a	chr6:30059640-30059650
39	NFYB	chr6:30059488-30060184	Hela-S3	cervix:	n/a	n/a
40	SMC3	chr6:30059460-30059903	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30059663..30061808-chr6:30067229..30070058,2	K562	blood:
2	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
3	chr6:30058142..30060356-chr6:30062997..30064640,2	MCF-7	breast:
4	chr6:30041901..30046365-chr6:30059553..30065121,9	MCF-7	breast:
5	chr6:30058600..30061539-chr6:30062741..30064895,3	MCF-7	breast:
6	chr6:30054428..30057425-chr6:30058219..30060222,2	MCF-7	breast:
7	chr6:30039555..30048654-chr6:30056865..30065735,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252901	TF binding region
ENSG00000252901	Chromatin interaction
ENSG00000204618	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv884052	chr6:30059592-30067681	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv884053	chr6:30059592-30070538	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30058400-30062200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:30058600-30060400	Enhancers	NHDF-Ad	bronchial
3	chr6:30058600-30061000	Enhancers	Fetal Intestine Small	intestine
4	chr6:30058600-30061400	Enhancers	Fetal Intestine Large	intestine
5	chr6:30058800-30060200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:30058800-30060200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:30058800-30060200	Enhancers	Spleen	Spleen
8	chr6:30059000-30060000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:30059000-30060000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:30059000-30060200	Enhancers	Esophagus	oesophagus
11	chr6:30059000-30060200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
12	chr6:30059000-30060200	Enhancers	HSMM	muscle
13	chr6:30059000-30060200	Enhancers	Osteobl	bone
14	chr6:30059000-30060400	Enhancers	Adipose Nuclei	Adipose
15	chr6:30059200-30060200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr6:30059200-30060200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr6:30059200-30060200	Enhancers	NHEK	skin
18	chr6:30059400-30060000	Enhancers	H1 Cell Line	embryonic stem cell
19	chr6:30059400-30060000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:30059400-30060000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:30059400-30060000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:30059400-30060000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:30059400-30060000	Bivalent Enhancer	Fetal Muscle Leg	muscle
24	chr6:30059400-30060000	Enhancers	A549	lung
25	chr6:30059400-30060200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
26	chr6:30059400-30060200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:30059400-30060200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:30059400-30060200	Flanking Active TSS	Hela-S3	cervix
29	chr6:30059400-30060200	Flanking Bivalent TSS/Enh	HepG2	liver
30	chr6:30059400-30060200	Enhancers	HMEC	breast
31	chr6:30059400-30060200	Enhancers	HSMMtube	muscle
32	chr6:30059400-30060200	Bivalent Enhancer	NHLF	lung
33	chr6:30059600-30060000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:30059600-30060000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
35	chr6:30059600-30060000	Enhancers	Gastric	stomach
36	chr6:30059600-30060000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr6:30059600-30060000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
38	chr6:30059600-30060200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:30059600-30060200	Enhancers	Pancreas	Pancrea
40	chr6:30059600-30060200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
41	chr6:30059600-30060200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
42	chr6:30059800-30060000	Flanking Bivalent TSS/Enh	ES-WA7 Cell Line	embryonic stem cell
43	chr6:30059800-30060000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
44	chr6:30059800-30060000	Flanking Bivalent TSS/Enh	Placenta	Placenta
45	chr6:30059800-30060000	Flanking Active TSS	Stomach Mucosa	stomach
46	chr6:30059800-30060200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:30059800-30060400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:30059800-30060400	Bivalent Enhancer	Duodenum Mucosa	Duodenum

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