Variant report

Variant	rs6909014
Chromosome Location	chr6:25279158-25279159
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	CTCF	chr6:25279145-25279349	GM10248	blood:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
2	MAX	chr6:25279099-25279820	K562	blood:	n/a	n/a
3	EP300	chr6:25279055-25279412	SK-N-SH_RA	brain:	n/a	n/a
4	RAD21	chr6:25278836-25280683	HCT-116	colon:	n/a	chr6:25279244-25279263 chr6:25279247-25279260 chr6:25279245-25279259
5	KAP1	chr6:25278193-25279426	HEK293	kidney:	n/a	n/a
6	POLR2A	chr6:25279059-25279620	U87	brain:	n/a	n/a
7	CTCF	chr6:25279131-25279428	MCF-7	breast:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
8	CTCF	chr6:25279143-25279343	MCF-7	breast:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
9	SIN3AK20	chr6:25279019-25279779	MCF-7	breast:	n/a	n/a
10	SMC3	chr6:25278958-25279740	GM12878	blood:	n/a	chr6:25279245-25279259
11	USF2	chr6:25278941-25279339	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr6:25279036-25279833	IMR90	lung:	n/a	n/a
13	RAD21	chr6:25279144-25279337	K562	blood:	n/a	chr6:25279244-25279263 chr6:25279247-25279260 chr6:25279245-25279259
14	ZNF143	chr6:25279012-25279485	Hela-S3	cervix:	n/a	n/a
15	GABPA	chr6:25279094-25279896	MCF-7	breast:	n/a	n/a
16	SMC3	chr6:25278594-25281162	Hela-S3	cervix:	n/a	chr6:25279245-25279259
17	POLR2A	chr6:25278931-25280140	MCF-7	breast:	n/a	n/a
18	RXRA	chr6:25279072-25279488	H1-hESC	embryonic stem cell:	n/a	n/a
19	RAD21	chr6:25278997-25279452	ECC-1	luminal epithelium:	n/a	chr6:25279244-25279263 chr6:25279247-25279260 chr6:25279245-25279259
20	FOS	chr6:25278944-25279854	HUVEC	blood vessel:	n/a	n/a
21	CTCF	chr6:25279124-25279369	GM10266	blood:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
22	MAFK	chr6:25278868-25279218	HepG2	liver:	n/a	chr6:25279029-25279044
23	YY1	chr6:25278998-25279905	HepG2	liver:	n/a	n/a
24	POLR2A	chr6:25278817-25280232	MCF10A-Er-Src	breast:	n/a	n/a
25	CTCF	chr6:25279118-25279386	ProgFib	skin:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
26	POLR2A	chr6:25279116-25279970	Gliobla	brain:	n/a	n/a
27	CTCF	chr6:25279101-25279400	Gliobla	brain:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
28	CEBPB	chr6:25279143-25279474	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr6:25278926-25280681	Hela-S3	cervix:	n/a	n/a
30	PML	chr6:25279069-25279717	MCF-7	breast:	n/a	n/a
31	YY1	chr6:25279157-25279344	K562	blood:	n/a	n/a
32	ZNF143	chr6:25279145-25279403	K562	blood:	n/a	n/a
33	CTCF	chr6:25279123-25279364	SK-N-SH_RA	brain:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
34	PML	chr6:25279154-25279875	MCF-7	breast:	n/a	n/a
35	MAZ	chr6:25278838-25280886	GM12878	blood:	n/a	chr6:25280836-25280846 chr6:25280072-25280079
36	GATA2	chr6:25278361-25279446	SH-SY5Y	brain:	n/a	chr6:25278424-25278440 chr6:25278422-25278443 chr6:25278429-25278436 chr6:25278429-25278436 chr6:25278429-25278436 chr6:25278644-25278654
37	CTCF	chr6:25279113-25279367	LNCaP	prostate:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
38	CTCF	chr6:25279142-25279370	Lung_OC	lung:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
39	E2F6	chr6:25278905-25279843	K562	blood:	n/a	chr6:25279656-25279667
40	BRCA1	chr6:25278864-25279632	GM12878	blood:	n/a	chr6:25279268-25279277
41	MYC	chr6:25278910-25279828	MCF10A-Er-Src	breast:	n/a	n/a
42	MAZ	chr6:25278969-25280217	IMR90	lung:	n/a	chr6:25280072-25280079
43	SIN3A	chr6:25278685-25281577	H1-hESC	embryonic stem cell:	n/a	n/a
44	GTF2F1	chr6:25278796-25279628	Hela-S3	cervix:	n/a	n/a
45	MAX	chr6:25279074-25279827	GM12878	blood:	n/a	n/a
46	CTCF	chr6:25278993-25279505	MCF-7	breast:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
47	CTCF	chr6:25279140-25279290	GM12801	blood:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
48	MAZ	chr6:25279073-25279806	K562	blood:	n/a	n/a
49	POLR2A	chr6:25279027-25279863	ECC-1	luminal epithelium:	n/a	n/a
50	CREB1	chr6:25279013-25279898	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:25279140-25279190	CMK	blood:	n/a
2	chr6:25279140-25279190	AG04450	lung:	fetal
3	chr6:25279140-25279190	HAEpiC	amniotic membrane:	n/a
4	chr6:25279140-25279190	AG09319	gingival:	n/a
5	chr6:25279140-25279190	GM12891	blood:	n/a
6	chr6:25279140-25279190	U87	brain:	n/a
7	chr6:25279140-25279190	HUVEC	blood vessel:	n/a
8	chr6:25279140-25279190	AG10803	skin:	n/a
9	chr6:25279140-25279190	IMR90	lung:	fetal
10	chr6:25279140-25279190	H1-hESC	embryonic stem cell:	embryo
11	chr6:25279140-25279190	NT2-D1	testis:	n/a
12	chr6:25279140-25279190	HRE	kidney:	n/a
13	chr6:25279140-25279190	SK-N-SH	brain:	n/a
14	chr6:25279140-25279190	HCF	heart:	n/a
15	chr6:25279140-25279190	HCT-116	colon:	n/a
16	chr6:25279140-25279190	LNCaP	prostate:	n/a
17	chr6:25279140-25279190	RPTEC	kidney:	n/a
18	chr6:25279140-25279190	GM06990	blood:	n/a
19	chr6:25279140-25279190	K562	blood:	n/a
20	chr6:25279140-25279190	SKMC	muscle:	n/a
21	chr6:25279140-25279190	BE2_C	brain:	n/a
22	chr6:25279140-25279190	NB4	blood:	n/a
23	chr6:25279140-25279190	Hela-S3	cervix:	n/a
24	chr6:25279140-25279190	T-47D	breast:	n/a
25	chr6:25279140-25279190	SK-N-SH_RA	brain:	n/a
26	chr6:25279140-25279190	GM19239	blood:	n/a
27	chr6:25279140-25279190	NHBE	bronchial:	n/a
28	chr6:25279140-25279190	ovcar-3	ovarian:	n/a
29	chr6:25279140-25279190	HepG2	liver:	n/a
30	chr6:25279140-25279190	HEK293	kidney:	embryo
31	chr6:25279140-25279190	A549	lung:	n/a
32	chr6:25279140-25279190	HRPEpiC	eye:	n/a
33	chr6:25279140-25279190	Jurkat	blood:	n/a
34	chr6:25279140-25279190	NHDF-neo	bronchial:	n/a
35	chr6:25279140-25279190	AG09309	skin:	n/a
36	chr6:25279140-25279190	PFSK-1	brain:	n/a
37	chr6:25279140-25279190	HRCEpiC	kidney:	n/a
38	chr6:25279140-25279190	HIPEpiC	eye:	n/a
39	chr6:25279140-25279190	AG04449	skin:	fetal
40	chr6:25279140-25279190	HPAEpiC	pulmonary alveolar:	n/a
41	chr6:25279140-25279190	HNPCEpiC	eye:	n/a
42	chr6:25279140-25279190	BJ	skin:	n/a
43	chr6:25279140-25279190	PrEC	prostate:	n/a
44	chr6:25279140-25279190	SAEC	small airway:	n/a
45	chr6:25279140-25279190	MCF-7	breast:	n/a
46	chr6:25279140-25279190	PANC-1	pancreas:	n/a
47	chr6:25279140-25279190	HEEpiC	esophagus:	n/a
48	chr6:25279140-25279190	ECC-1	luminal epithelium:	n/a
49	chr6:25279140-25279190	ProgFib	skin:	n/a
50	chr6:25279140-25279190	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:25277631..25279275-chr6:25301822..25304144,2	MCF-7	breast:
2	chr6:25277929..25281528-chr6:25281560..25287992,8	MCF-7	breast:
3	chr6:25277697..25280622-chr6:25286931..25288666,2	MCF-7	breast:

Variant related genes	Relation type
LRRC16A	TF binding region
LRRC16A	CpG island
ENSG00000207286	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1016855	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690054	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2690061	0.86[EUR][1000 genomes]
rs2690064	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2690067	0.85[EUR][1000 genomes]
rs2744254	0.83[EUR][1000 genomes]
rs2744257	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2744258	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2744267	0.94[EUR][1000 genomes]
rs2744268	0.86[EUR][1000 genomes]
rs2744269	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6908902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914799	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6926126	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs721037	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs723048	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9358848	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393635	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS 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	43 gene(s)	inside rSNPs	diseases
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr6:25278200-25279200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:25278400-25279200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:25278400-25279200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr6:25278400-25279200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:25278400-25279200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:25278400-25279200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
7	chr6:25278400-25279200	Flanking Bivalent TSS/Enh	HepG2	liver
8	chr6:25278400-25279200	Flanking Active TSS	NHEK	skin
9	chr6:25278400-25280000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:25278400-25280800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:25278400-25281600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:25278400-25281600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr6:25278400-25281600	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr6:25278600-25279200	Flanking Active TSS	Primary B cells from peripheral blood	blood
15	chr6:25278600-25279200	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr6:25278600-25279200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
17	chr6:25278600-25279200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr6:25278600-25279200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr6:25278600-25279200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:25278600-25279200	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr6:25278600-25279200	Flanking Active TSS	Liver	Liver
22	chr6:25278600-25279200	Flanking Active TSS	Brain Substantia Nigra	brain
23	chr6:25278600-25279200	Flanking Active TSS	Fetal Brain Male	brain
24	chr6:25278600-25279200	Flanking Active TSS	Fetal Stomach	stomach
25	chr6:25278600-25279200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
26	chr6:25278600-25279200	Flanking Active TSS	Thymus	Thymus
27	chr6:25278600-25279200	Flanking Active TSS	HSMMtube	muscle
28	chr6:25278600-25279200	Flanking Active TSS	Osteobl	bone
29	chr6:25278600-25280200	Flanking Bivalent TSS/Enh	Dnd41	blood
30	chr6:25278600-25280400	Active TSS	Brain Germinal Matrix	brain
31	chr6:25278600-25280600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:25278600-25281000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:25278600-25281000	Active TSS	A549	lung
34	chr6:25278600-25281200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:25278600-25281400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr6:25278600-25281400	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr6:25278600-25281400	Active TSS	Right Ventricle	heart
38	chr6:25278600-25283400	Active TSS	Aorta	Aorta
39	chr6:25278800-25279200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:25278800-25279200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr6:25278800-25279200	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:25278800-25279200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr6:25278800-25279200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr6:25278800-25279200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:25278800-25279200	Flanking Active TSS	Brain Angular Gyrus	brain
46	chr6:25278800-25279200	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr6:25278800-25279200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr6:25278800-25279200	Flanking Active TSS	Fetal Heart	heart
49	chr6:25278800-25279200	Flanking Active TSS	Fetal Thymus	thymus
50	chr6:25278800-25279200	Flanking Active TSS	HUVEC	blood vessel

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