Variant report

Variant	rs6569075
Chromosome Location	chr6:119672331-119672332
allele	A/G
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	chr6:119672200-119672350	AG09309	skin:	n/a	chr6:119672266-119672284
2	CTCF	chr6:119672164-119672349	GM13976	blood:	n/a	chr6:119672266-119672284
3	EBF1	chr6:119672252-119672459	GM12878	blood:	n/a	n/a
4	RAD21	chr6:119671943-119672637	MCF-7	breast:	n/a	chr6:119672267-119672286
5	CTCF	chr6:119672152-119672386	Medullo	brain:	n/a	chr6:119672266-119672284
6	CTCF	chr6:119672220-119672370	HCM	heart:	n/a	chr6:119672266-119672284
7	CTCF	chr6:119672220-119672370	MCF-7	breast:	n/a	chr6:119672266-119672284
8	CTCF	chr6:119672220-119672370	GM12874	blood:	n/a	chr6:119672266-119672284
9	CTCF	chr6:119672163-119672358	GM10266	blood:	n/a	chr6:119672266-119672284
10	MTA3	chr6:119670171-119672498	GM12878	blood:	n/a	n/a
11	CTCF	chr6:119672280-119672430	RPTEC	kidney:	n/a	n/a
12	CTCF	chr6:119671898-119672488	IMR90	lung:	n/a	chr6:119672266-119672284
13	IRF1	chr6:119670460-119672556	K562	blood:	n/a	chr6:119671026-119671040 chr6:119671674-119671688 chr6:119671673-119671685 chr6:119672317-119672331 chr6:119671673-119671685
14	NFATC1	chr6:119671282-119672574	GM12878	blood:	n/a	n/a
15	CTCF	chr6:119672200-119672350	GM12864	blood:	n/a	chr6:119672266-119672284
16	RAD21	chr6:119671480-119672616	HCT-116	colon:	n/a	chr6:119672267-119672286
17	RAD21	chr6:119672166-119672452	H1-hESC	embryonic stem cell:	n/a	chr6:119672267-119672286
18	CTCF	chr6:119672240-119672390	BE2_C	brain:	n/a	chr6:119672266-119672284
19	CHD1	chr6:119670735-119672402	GM12878	blood:	n/a	chr6:119671060-119671070 chr6:119671143-119671153
20	CTCF	chr6:119672280-119672430	HAc	cerebellar:	n/a	n/a
21	CTCF	chr6:119672200-119672350	WI-38	lung:	n/a	chr6:119672266-119672284
22	BHLHE40	chr6:119670357-119672411	GM12878	blood:	n/a	n/a
23	IRF1	chr6:119671502-119672514	K562	blood:	n/a	chr6:119671674-119671688 chr6:119671673-119671685 chr6:119672317-119672331 chr6:119671673-119671685
24	SMC3	chr6:119671498-119672517	GM12878	blood:	n/a	n/a
25	CTCF	chr6:119672240-119672390	MCF-7	breast:	n/a	chr6:119672266-119672284
26	SMC3	chr6:119671775-119672453	K562	blood:	n/a	n/a
27	FOXM1	chr6:119671397-119672500	GM12878	blood:	n/a	n/a
28	RAD21	chr6:119672099-119672474	Hela-S3	cervix:	n/a	chr6:119672267-119672286
29	TEAD4	chr6:119671509-119672477	K562	blood:	n/a	n/a
30	ARID3A	chr6:119671876-119672527	K562	blood:	n/a	n/a
31	CTCF	chr6:119672240-119672390	SAEC	small airway:	n/a	chr6:119672266-119672284
32	EP300	chr6:119671713-119672459	K562	blood:	n/a	chr6:119671847-119671855
33	CTCF	chr6:119672140-119672401	SK-N-SH_RA	brain:	n/a	chr6:119672266-119672284
34	CTCF	chr6:119672220-119672370	GM12871	blood:	n/a	chr6:119672266-119672284
35	CTCF	chr6:119672200-119672350	HA-sp	spinal cord:	n/a	chr6:119672266-119672284
36	CTCF	chr6:119672180-119672361	GM13977	blood:	n/a	chr6:119672266-119672284
37	CTCF	chr6:119672240-119672390	GM12868	blood:	n/a	chr6:119672266-119672284
38	ARID3A	chr6:119671696-119672498	HepG2	liver:	n/a	n/a
39	CTCF	chr6:119672200-119672350	AG10803	skin:	n/a	chr6:119672266-119672284
40	CTCF	chr6:119672167-119672368	Pancreas_OC	pancreas:	n/a	chr6:119672266-119672284
41	ATF2	chr6:119671419-119672459	GM12878	blood:	n/a	n/a
42	CTCF	chr6:119672220-119672370	HCT-116	colon:	n/a	chr6:119672266-119672284
43	CTCF	chr6:119672220-119672370	GM12867	blood:	n/a	chr6:119672266-119672284
44	CTCF	chr6:119672240-119672390	GM12872	blood:	n/a	chr6:119672266-119672284
45	CTCF	chr6:119672170-119672382	K562	blood:	n/a	chr6:119672266-119672284
46	CTCF	chr6:119672164-119672368	GM10248	blood:	n/a	chr6:119672266-119672284
47	CTCF	chr6:119670364-119672561	SK-N-SH	brain:	n/a	chr6:119670437-119670450 chr6:119672266-119672284
48	CTCF	chr6:119672160-119672450	HCT-116	colon:	n/a	chr6:119672266-119672284
49	CTCF	chr6:119672240-119672390	RPTEC	kidney:	n/a	chr6:119672266-119672284
50	SMC3	chr6:119671974-119672453	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:119672022..119674199-chr6:119758005..119760805,2	K562	blood:
2	chr6:119671918..119674788-chr6:119887253..119890815,3	K562	blood:
3	chr6:119671114..119672646-chr6:119674979..119676830,2	K562	blood:
4	chr6:119672013..119673018-chr6:120041067..120041943,4	MCF-7	breast:
5	chr6:119671889..119672806-chr6:120299171..120300057,2	MCF-7	breast:
6	chr6:119671920..119673438-chr6:119680108..119682545,2	K562	blood:
7	chr6:119671503..119673094-chr6:120039219..120042156,2	K562	blood:
8	chr6:119671114..119673053-chr6:119674972..119676830,3	K562	blood:
9	chr6:119668881..119671932-chr6:119672214..119675857,4	MCF-7	breast:
10	chr6:119671568..119672634-chr6:120040996..120041889,3	MCF-7	breast:
11	chr6:119671974..119673513-chr6:122790759..122793728,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASF1A-6	chr6:119671256-119673798	NONHSAT114714

Variant related genes	Relation type
MAN1A1	TF binding region
ENSG00000135549	Chromatin interaction
ENSG00000111885	Chromatin interaction
ENSG00000111897	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11153813	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1295379	0.87[ASN][1000 genomes]
rs1295386	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1295390	0.87[ASN][1000 genomes]
rs1295392	0.87[AFR][1000 genomes]
rs1298630	0.82[ASN][1000 genomes]
rs1342316	0.82[ASN][1000 genomes]
rs1797064	0.88[ASN][1000 genomes]
rs195046	0.82[ASN][1000 genomes]
rs195051	0.82[ASN][1000 genomes]
rs195062	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs195063	0.84[ASN][1000 genomes]
rs195071	0.93[ASN][1000 genomes]
rs195076	0.84[ASN][1000 genomes]
rs195078	0.93[ASN][1000 genomes]
rs195079	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs195081	0.84[ASN][1000 genomes]
rs195083	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs195086	0.87[ASN][1000 genomes]
rs195088	0.82[ASN][1000 genomes]
rs195091	0.82[ASN][1000 genomes]
rs4945633	0.81[ASN][1000 genomes]
rs4946409	0.89[ASN][1000 genomes]
rs6569063	0.81[ASN][1000 genomes]
rs6569074	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6921356	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6924723	0.90[ASN][1000 genomes]
rs7765368	0.88[ASN][1000 genomes]
rs7773367	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9320684	0.81[ASN][1000 genomes]
rs9372527	0.80[ASN][1000 genomes]
rs9374791	0.82[ASN][1000 genomes]
rs9387646	0.83[ASN][1000 genomes]
rs9489654	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv1802628	chr6:119647135-119678881	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119664800-119672400	Active TSS	Brain Anterior Caudate	brain
2	chr6:119665200-119672800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:119666200-119672600	Active TSS	NHDF-Ad	bronchial
4	chr6:119666600-119672400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr6:119667000-119672400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:119667000-119672400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:119667000-119672800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:119667200-119672400	Active TSS	Right Atrium	heart
9	chr6:119668200-119672600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:119668200-119672600	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr6:119669000-119672400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:119669000-119672400	Active TSS	Placenta Amnion	Placenta Amnion
13	chr6:119669400-119672400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr6:119669400-119672400	Active TSS	Stomach Smooth Muscle	stomach
15	chr6:119669400-119673000	Active TSS	GM12878-XiMat	blood
16	chr6:119669600-119672400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:119669600-119673000	Active TSS	Adipose Nuclei	Adipose
18	chr6:119669600-119673000	Active TSS	K562	blood
19	chr6:119669800-119672800	Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:119670800-119672400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:119671000-119672400	Active TSS	Brain Hippocampus Middle	brain
22	chr6:119671200-119672600	Flanking Bivalent TSS/Enh	Dnd41	blood
23	chr6:119671400-119672400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:119671600-119672400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr6:119671600-119672400	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr6:119671600-119672400	Flanking Active TSS	Liver	Liver
27	chr6:119671600-119672400	Bivalent/Poised TSS	Fetal Brain Male	brain
28	chr6:119671600-119672600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:119671800-119672400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:119671800-119672400	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr6:119671800-119672400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr6:119671800-119672400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr6:119671800-119672400	Flanking Active TSS	NHEK	skin
34	chr6:119671800-119672600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:119671800-119673400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:119671800-119689200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:119672000-119672400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:119672000-119672400	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr6:119672000-119672400	Active TSS	HepG2	liver
40	chr6:119672000-119673000	Weak transcription	Fetal Heart	heart
41	chr6:119672000-119673400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr6:119672000-119674400	Weak transcription	Small Intestine	intestine
43	chr6:119672000-119674600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr6:119672000-119675000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:119672200-119672400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
46	chr6:119672200-119672400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr6:119672200-119672400	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr6:119672200-119672400	Enhancers	Primary B cells from peripheral blood	blood
49	chr6:119672200-119672400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr6:119672200-119672400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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