Variant report

Variant	rs2690104
Chromosome Location	chr6:25279227-25279228
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	CTCF	chr6:25279180-25279330	Caco-2	colon:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
3	MAX	chr6:25279099-25279820	K562	blood:	n/a	n/a
4	EP300	chr6:25279055-25279412	SK-N-SH_RA	brain:	n/a	n/a
5	RAD21	chr6:25278836-25280683	HCT-116	colon:	n/a	chr6:25279244-25279263 chr6:25279247-25279260 chr6:25279245-25279259
6	CTCF	chr6:25279180-25279330	GM12872	blood:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
7	KAP1	chr6:25278193-25279426	HEK293	kidney:	n/a	n/a
8	POLR2A	chr6:25279059-25279620	U87	brain:	n/a	n/a
9	CTCF	chr6:25279131-25279428	MCF-7	breast:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
10	CTCF	chr6:25279160-25279310	AG04450	lung:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
11	CTCF	chr6:25279143-25279343	MCF-7	breast:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
12	SIN3AK20	chr6:25279019-25279779	MCF-7	breast:	n/a	n/a
13	BHLHE40	chr6:25279190-25279380	K562	blood:	n/a	n/a
14	SMC3	chr6:25278958-25279740	GM12878	blood:	n/a	chr6:25279245-25279259
15	USF2	chr6:25278941-25279339	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:25279036-25279833	IMR90	lung:	n/a	n/a
17	RAD21	chr6:25279144-25279337	K562	blood:	n/a	chr6:25279244-25279263 chr6:25279247-25279260 chr6:25279245-25279259
18	ZNF143	chr6:25279012-25279485	Hela-S3	cervix:	n/a	n/a
19	GABPA	chr6:25279094-25279896	MCF-7	breast:	n/a	n/a
20	SMC3	chr6:25278594-25281162	Hela-S3	cervix:	n/a	chr6:25279245-25279259
21	MYC	chr6:25279214-25279832	MCF-7	breast:	n/a	n/a
22	POLR2A	chr6:25278931-25280140	MCF-7	breast:	n/a	n/a
23	CTCF	chr6:25279180-25279330	NHDF-neo	bronchial:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
24	RXRA	chr6:25279072-25279488	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr6:25279160-25279310	WERI-Rb-1	eye:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
26	CTCF	chr6:25279180-25279330	AoAF	blood vessel:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
27	RAD21	chr6:25278997-25279452	ECC-1	luminal epithelium:	n/a	chr6:25279244-25279263 chr6:25279247-25279260 chr6:25279245-25279259
28	FOS	chr6:25278944-25279854	HUVEC	blood vessel:	n/a	n/a
29	CTCF	chr6:25279124-25279369	GM10266	blood:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
30	YY1	chr6:25278998-25279905	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:25278817-25280232	MCF10A-Er-Src	breast:	n/a	n/a
32	CTCF	chr6:25279118-25279386	ProgFib	skin:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
33	POLR2A	chr6:25279116-25279970	Gliobla	brain:	n/a	n/a
34	CTCF	chr6:25279101-25279400	Gliobla	brain:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
35	CEBPB	chr6:25279143-25279474	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr6:25279200-25279350	HAc	cerebellar:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
37	POLR2A	chr6:25279187-25279505	HUVEC	blood vessel:	n/a	n/a
38	EP300	chr6:25279167-25279484	SK-N-SH_RA	brain:	n/a	n/a
39	POLR2A	chr6:25279206-25279905	Raji	blood:	n/a	n/a
40	POLR2A	chr6:25278926-25280681	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr6:25279200-25279350	HepG2	liver:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
42	PML	chr6:25279069-25279717	MCF-7	breast:	n/a	n/a
43	YY1	chr6:25279157-25279344	K562	blood:	n/a	n/a
44	ZNF143	chr6:25279145-25279403	K562	blood:	n/a	n/a
45	CTCF	chr6:25279180-25279330	WERI-Rb-1	eye:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
46	CTCF	chr6:25279123-25279364	SK-N-SH_RA	brain:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
47	CTCFL	chr6:25279174-25279356	K562	blood:	n/a	n/a
48	PML	chr6:25279154-25279875	MCF-7	breast:	n/a	n/a
49	CTCF	chr6:25279160-25279310	AoAF	blood vessel:	n/a	chr6:25279243-25279261 chr6:25279245-25279266 chr6:25279246-25279259
50	MAZ	chr6:25278838-25280886	GM12878	blood:	n/a	chr6:25280836-25280846 chr6:25280072-25280079

No.	Distal block	Cell Line	Cell type
1	chr6:25277631..25279275-chr6:25301822..25304144,2	MCF-7	breast:
2	chr6:25201388..25203909-chr6:25279159..25280911,2	MCF-7	breast:
3	chr6:25277929..25281528-chr6:25281560..25287992,8	MCF-7	breast:
4	chr6:25277697..25280622-chr6:25286931..25288666,2	MCF-7	breast:

Variant related genes	Relation type
LRRC16A	TF binding region
ENSG00000207286	Chromatin interaction
ENSG00000264238	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs16890271	1.00[ASN][1000 genomes]
rs1815097	1.00[ASN][1000 genomes]
rs2328869	0.86[EUR][1000 genomes]
rs2690043	1.00[ASN][1000 genomes]
rs2690044	1.00[ASN][1000 genomes]
rs2690045	1.00[ASN][1000 genomes]
rs2690046	1.00[ASN][1000 genomes]
rs2690048	1.00[ASN][1000 genomes]
rs2690049	1.00[ASN][1000 genomes]
rs2690050	1.00[ASN][1000 genomes]
rs2690051	1.00[ASN][1000 genomes]
rs2690052	1.00[ASN][1000 genomes]
rs2690055	1.00[ASN][1000 genomes]
rs2690057	1.00[ASN][1000 genomes]
rs2690058	1.00[ASN][1000 genomes]
rs2690063	1.00[ASN][1000 genomes]
rs2690066	1.00[ASN][1000 genomes]
rs2690069	1.00[ASN][1000 genomes]
rs2690102	1.00[ASN][1000 genomes]
rs2744255	1.00[ASN][1000 genomes]
rs2744259	1.00[ASN][1000 genomes]
rs2744260	1.00[ASN][1000 genomes]
rs2744263	1.00[ASN][1000 genomes]
rs2744265	1.00[ASN][1000 genomes]
rs2744266	1.00[ASN][1000 genomes]
rs2744275	1.00[ASN][1000 genomes]
rs2744276	1.00[ASN][1000 genomes]
rs2744277	1.00[ASN][1000 genomes]
rs2744278	1.00[ASN][1000 genomes]
rs2744279	1.00[ASN][1000 genomes]
rs2744280	1.00[ASN][1000 genomes]
rs2744282	1.00[ASN][1000 genomes]
rs2744284	1.00[ASN][1000 genomes]
rs2744285	1.00[ASN][1000 genomes]
rs2744286	1.00[ASN][1000 genomes]
rs6456661	0.86[EUR][1000 genomes]
rs6936169	0.83[EUR][1000 genomes]
rs7743997	1.00[ASN][1000 genomes]
rs7767189	1.00[ASN][1000 genomes]
rs940405	1.00[ASN][1000 genomes]
rs9688905	1.00[ASN][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	chr6:25278400-25280000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:25278400-25280800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:25278400-25281600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr6:25278400-25281600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr6:25278400-25281600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:25278600-25280200	Flanking Bivalent TSS/Enh	Dnd41	blood
7	chr6:25278600-25280400	Active TSS	Brain Germinal Matrix	brain
8	chr6:25278600-25280600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:25278600-25281000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:25278600-25281000	Active TSS	A549	lung
11	chr6:25278600-25281200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:25278600-25281400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr6:25278600-25281400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr6:25278600-25281400	Active TSS	Right Ventricle	heart
15	chr6:25278600-25283400	Active TSS	Aorta	Aorta
16	chr6:25278800-25279400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:25278800-25279400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
18	chr6:25278800-25280000	Active TSS	Duodenum Mucosa	Duodenum
19	chr6:25278800-25280000	Active TSS	Fetal Brain Female	brain
20	chr6:25278800-25280000	Active TSS	Lung	lung
21	chr6:25278800-25280200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:25278800-25280400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:25278800-25280400	Active TSS	Stomach Mucosa	stomach
24	chr6:25278800-25280600	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr6:25278800-25280600	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr6:25278800-25280800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:25278800-25280800	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr6:25278800-25281000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:25278800-25281000	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr6:25278800-25281000	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr6:25278800-25281000	Active TSS	Placenta Amnion	Placenta Amnion
32	chr6:25278800-25281200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:25278800-25281200	Active TSS	Esophagus	oesophagus
34	chr6:25278800-25281200	Active TSS	Ovary	ovary
35	chr6:25278800-25281400	Active TSS	Fetal Kidney	kidney
36	chr6:25278800-25281600	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr6:25278800-25281600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr6:25278800-25281600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:25278800-25281600	Active TSS	Right Atrium	heart
40	chr6:25279000-25279400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
41	chr6:25279000-25279400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr6:25279000-25279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:25279000-25279600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr6:25279000-25279800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:25279000-25279800	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr6:25279000-25279800	Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr6:25279000-25279800	Active TSS	Fetal Muscle Trunk	muscle
48	chr6:25279000-25279800	Active TSS	Placenta	Placenta
49	chr6:25279000-25280000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:25279000-25280000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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