Variant report

Variant	rs541385052
Chromosome Location	chr6:15249623-15249624
allele	-/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	chr6:15248652-15249654	HCT-116	colon:	n/a	n/a
2	POLR2A	chr6:15248962-15249742	GM12892	blood:	n/a	n/a
3	ELF1	chr6:15248664-15249712	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:15247950-15249674	H1-neurons	neurons:	n/a	n/a
5	BRCA1	chr6:15248771-15249972	Hela-S3	cervix:	n/a	n/a
6	CREB1	chr6:15247870-15249858	GM12878	blood:	n/a	chr6:15248972-15248985 chr6:15249021-15249034
7	POLR2A	chr6:15248696-15249648	HL-60	blood:	n/a	n/a
8	MAX	chr6:15248705-15249672	SK-N-SH	brain:	n/a	n/a
9	CREB1	chr6:15248155-15249672	HepG2	liver:	n/a	chr6:15248972-15248985 chr6:15249021-15249034
10	CREB1	chr6:15247845-15250008	K562	blood:	n/a	chr6:15248972-15248985 chr6:15249021-15249034
11	MAX	chr6:15247952-15249665	HepG2	liver:	n/a	n/a
12	MTA3	chr6:15249165-15249863	GM12878	blood:	n/a	n/a
13	MTA3	chr6:15248694-15250134	GM12878	blood:	n/a	n/a
14	MXI1	chr6:15248838-15250074	GM12878	blood:	n/a	n/a
15	ELF1	chr6:15248739-15249656	K562	blood:	n/a	n/a
16	POLR2A	chr6:15249087-15249671	GM12891	blood:	n/a	n/a
17	YY1	chr6:15249347-15249634	GM12878	blood:	n/a	n/a
18	SMC3	chr6:15248813-15250273	Hela-S3	cervix:	n/a	n/a
19	MAX	chr6:15248677-15249744	MCF-7	breast:	n/a	n/a
20	POLR2A	chr6:15248088-15249623	GM19099	blood:	n/a	n/a
21	HCFC1	chr6:15244775-15250295	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr6:15248082-15249646	GM15510	blood:	n/a	n/a
23	POLR2A	chr6:15248656-15249743	GM12892	blood:	n/a	n/a
24	CHD1	chr6:15244739-15251552	IMR90	lung:	n/a	chr6:15245627-15245637 chr6:15245113-15245123
25	RCOR1	chr6:15248757-15249743	GM12878	blood:	n/a	n/a
26	FOXM1	chr6:15248828-15249755	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:15248712-15249854	SK-N-MC	brain:	n/a	n/a
28	REST	chr6:15247751-15250156	H1-neurons	neurons:	n/a	chr6:15249880-15249888 chr6:15249689-15249697 chr6:15249264-15249274
29	RCOR1	chr6:15248715-15249743	K562	blood:	n/a	n/a
30	MYC	chr6:15249200-15250181	MCF10A-Er-Src	breast:	n/a	n/a
31	MAX	chr6:15248710-15249959	NB4	blood:	n/a	n/a
32	MAX	chr6:15248670-15249721	HepG2	liver:	n/a	n/a
33	ELK1	chr6:15249163-15249646	GM12878	blood:	n/a	n/a
34	POLR2A	chr6:15248689-15249630	K562	blood:	n/a	n/a
35	TCF7L2	chr6:15248684-15249690	HCT-116	colon:	n/a	n/a
36	POLR2A	chr6:15247896-15249740	H1-neurons	neurons:	n/a	n/a
37	POLR2A	chr6:15247966-15250036	Hela-S3	cervix:	n/a	n/a
38	MYC	chr6:15248651-15249925	K562	blood:	n/a	n/a
39	STAT5A	chr6:15248731-15249978	GM12878	blood:	n/a	chr6:15249387-15249398
40	JUN	chr6:15248675-15250516	K562	blood:	n/a	chr6:15249266-15249275 chr6:15248974-15248983
41	TBP	chr6:15248708-15249836	K562	blood:	n/a	n/a
42	POLR2A	chr6:15249073-15249804	GM12878	blood:	n/a	n/a
43	CREB1	chr6:15248659-15249726	GM12878	blood:	n/a	chr6:15248972-15248985 chr6:15249021-15249034
44	RAD21	chr6:15249310-15249760	GM12878	blood:	n/a	n/a
45	MAX	chr6:15248629-15249644	K562	blood:	n/a	n/a
46	CBX3	chr6:15248648-15249734	K562	blood:	n/a	n/a
47	POLR2A	chr6:15247994-15249711	HL-60	blood:	n/a	n/a
48	RELA	chr6:15248767-15249748	GM12891	blood:	n/a	chr6:15249569-15249578 chr6:15249569-15249578
49	MAX	chr6:15248737-15249649	ECC-1	luminal epithelium:	n/a	n/a
50	RUNX3	chr6:15248718-15250055	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:15248895..15250425-chr6:16129384..16130957,2	K562	blood:
2	chr18:57566476..57568620-chr6:15247479..15249980,2	K562	blood:
3	chr6:15155665..15157322-chr6:15249355..15251263,2	K562	blood:
4	chr6:15248004..15250330-chr6:15324617..15327935,3	K562	blood:
5	chr6:15087836..15090279-chr6:15247303..15249952,4	K562	blood:
6	chr10:103577822..103578398-chr6:15249181..15249836,2	Hela-S3	cervix:
7	chr6:15087697..15092455-chr6:15243972..15249952,11	K562	blood:
8	chr6:15247440..15249791-chr6:15324617..15327427,3	K562	blood:

Variant related genes	Relation type
ENSG00000271888	TF binding region
JARID2-AS1	TF binding region
ENSG00000007944	Chromatin interaction
ENSG00000198408	Chromatin interaction
ENSG00000234261	Chromatin interaction
ENSG00000201519	Chromatin interaction
ENSG00000141682	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830594	chr6:15171158-15261296	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1818166	chr6:15247393-15250052	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv3426622	chr6:15247498-15250346	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	esv3511820	chr6:15247723-15249971	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	esv3511821	chr6:15247723-15249971	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	esv3437390	chr6:15248023-15249771	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15243600-15250200	Active TSS	H9 Cell Line	embryonic stem cell
2	chr6:15244000-15250000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:15244200-15249800	Active TSS	Rectal Smooth Muscle	rectum
4	chr6:15244400-15250200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:15244400-15250400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:15244600-15249800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:15244600-15249800	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr6:15244600-15249800	Active TSS	Ovary	ovary
9	chr6:15244600-15249800	Active TSS	Psoas Muscle	Psoas
10	chr6:15244600-15250000	Active TSS	NHLF	lung
11	chr6:15244600-15250200	Active TSS	A549	lung
12	chr6:15244600-15250400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr6:15244800-15249800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:15244800-15249800	Active TSS	Aorta	Aorta
15	chr6:15244800-15249800	Active TSS	Esophagus	oesophagus
16	chr6:15244800-15250000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:15245000-15250000	Active TSS	Colonic Mucosa	Colon
18	chr6:15245000-15250800	Active TSS	GM12878-XiMat	blood
19	chr6:15245000-15251000	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr6:15245200-15250400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:15245400-15250800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:15247800-15250200	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr6:15249000-15250000	Flanking Active TSS	Fetal Brain Male	brain
24	chr6:15249000-15251800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:15249200-15249800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:15249200-15249800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
27	chr6:15249200-15249800	Flanking Active TSS	Primary B cells from peripheral blood	blood
28	chr6:15249200-15249800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:15249200-15249800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:15249200-15249800	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr6:15249200-15249800	Flanking Active TSS	HUVEC	blood vessel
32	chr6:15249200-15250000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr6:15249200-15250000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
34	chr6:15249200-15250000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:15249200-15250000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
36	chr6:15249200-15250000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr6:15249200-15250000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:15249200-15250000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr6:15249200-15250000	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr6:15249200-15250000	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr6:15249200-15250000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr6:15249200-15250000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr6:15249200-15250000	Active TSS	Right Atrium	heart
44	chr6:15249200-15250000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr6:15249200-15250000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr6:15249200-15250200	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr6:15249200-15250200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:15249200-15250200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:15249200-15250200	Flanking Active TSS	Fetal Thymus	thymus
50	chr6:15249200-15250200	Flanking Active TSS	HMEC	breast

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