Variant report

Variant	rs569453338
Chromosome Location	chr6:27782625-27782626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:248)
CpG islands
(count:61)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:248 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:27781476-27784189	ProgFib	skin:	n/a	n/a
2	NFIC	chr6:27782377-27782887	HepG2	liver:	n/a	n/a
3	PML	chr6:27782445-27783142	MCF-7	breast:	n/a	n/a
4	PML	chr6:27782350-27784057	GM12878	blood:	n/a	n/a
5	HA-E2F1	chr6:27782053-27782778	MCF-7	breast:	n/a	chr6:27782597-27782606 chr6:27782701-27782710 chr6:27782598-27782605 chr6:27782598-27782605 chr6:27782594-27782605 chr6:27782598-27782605 chr6:27782699-27782708 chr6:27782595-27782610
6	MAFK	chr6:27782562-27783013	Hela-S3	cervix:	n/a	n/a
7	SETDB1	chr6:27782544-27783270	U2OS	brain:	n/a	n/a
8	TBP	chr6:27782388-27782943	HepG2	liver:	n/a	n/a
9	ATF2	chr6:27782380-27782993	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr6:27781096-27784165	GM18505	blood:	n/a	n/a
11	FOS	chr6:27782481-27782900	GM12878	blood:	n/a	chr6:27782722-27782731 chr6:27782700-27782709
12	ZBTB33	chr6:27782429-27783489	SK-N-SH	brain:	n/a	n/a
13	CBX3	chr6:27782431-27783364	HCT-116	colon:	n/a	n/a
14	SP1	chr6:27782397-27783146	HCT-116	colon:	n/a	n/a
15	POLR2A	chr6:27781361-27783350	Hela-S3	cervix:	n/a	n/a
16	SP1	chr6:27782134-27783230	A549	lung:	n/a	n/a
17	RFX5	chr6:27782548-27783039	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:27781536-27783771	HUVEC	blood vessel:	n/a	n/a
19	SIN3AK20	chr6:27782618-27783359	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr6:27781320-27783475	U87	brain:	n/a	n/a
21	SP1	chr6:27782400-27783088	H1-hESC	embryonic stem cell:	n/a	n/a
22	FOSL2	chr6:27781949-27782702	HepG2	liver:	n/a	n/a
23	CREB1	chr6:27782433-27783064	H1-hESC	embryonic stem cell:	n/a	chr6:27782698-27782711
24	POLR2A	chr6:27779808-27783925	H1-hESC	embryonic stem cell:	n/a	n/a
25	JUND	chr6:27782486-27782869	Hela-S3	cervix:	n/a	chr6:27782722-27782731 chr6:27782700-27782709
26	MTA3	chr6:27782365-27783982	GM12878	blood:	n/a	n/a
27	CHD2	chr6:27782393-27783192	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr6:27781403-27783773	GM12891	blood:	n/a	n/a
29	POLR2A	chr6:27781745-27782632	Gliobla	brain:	n/a	n/a
30	FOS	chr6:27782518-27782838	MCF10A-Er-Src	breast:	n/a	chr6:27782722-27782731 chr6:27782700-27782709
31	REST	chr6:27782374-27783000	A549	lung:	n/a	n/a
32	POLR2A	chr6:27781061-27783247	Hela-S3	cervix:	n/a	n/a
33	FOSL2	chr6:27782073-27782698	HepG2	liver:	n/a	n/a
34	BATF	chr6:27782021-27782683	GM12878	blood:	n/a	n/a
35	MBD4	chr6:27782382-27783005	HepG2	liver:	n/a	n/a
36	JUND	chr6:27782158-27782683	A549	lung:	n/a	n/a
37	TBP	chr6:27782391-27783058	GM12878	blood:	n/a	n/a
38	FOXM1	chr6:27781391-27783896	GM12878	blood:	n/a	n/a
39	POLR2A	chr6:27781286-27783860	SK-N-SH	brain:	n/a	n/a
40	E2F4	chr6:27782373-27782909	MCF10A-Er-Src	breast:	n/a	chr6:27782597-27782606 chr6:27782701-27782710 chr6:27782598-27782605 chr6:27782598-27782605 chr6:27782594-27782605 chr6:27782598-27782605 chr6:27782699-27782708 chr6:27782595-27782610
41	SIN3AK20	chr6:27782102-27782654	HepG2	liver:	n/a	n/a
42	POLR2A	chr6:27781646-27783336	H1-hESC	embryonic stem cell:	n/a	n/a
43	ARID3A	chr6:27782504-27782940	HepG2	liver:	n/a	n/a
44	ELK1	chr6:27782514-27782884	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr6:27780777-27784258	GM12878	blood:	n/a	n/a
46	MYBL2	chr6:27781455-27783474	HepG2	liver:	n/a	n/a
47	POLR2A	chr6:27781498-27782898	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr6:27781970-27782625	A549	lung:	n/a	n/a
49	TEAD4	chr6:27781419-27783062	HepG2	liver:	n/a	n/a
50	POLR2A	chr6:27781293-27783971	SK-N-SH	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:27782617-27782667	Caco-2	colon:	n/a
2	chr6:27782617-27782667	NH-A	brain:	n/a
3	chr6:27782617-27782667	Hela-S3	cervix:	n/a
4	chr6:27782617-27782667	HNPCEpiC	eye:	n/a
5	chr6:27782617-27782667	Hepatocyte	liver:	n/a
6	chr6:27782617-27782667	HRPEpiC	eye:	n/a
7	chr6:27782617-27782667	PFSK-1	brain:	n/a
8	chr6:27782617-27782667	MCF10A-Er-Src	breast:	n/a
9	chr6:27782617-27782667	HEK293	kidney:	embryo
10	chr6:27782617-27782667	T-47D	breast:	n/a
11	chr6:27782617-27782667	GM19239	blood:	n/a
12	chr6:27782617-27782667	NB4	blood:	n/a
13	chr6:27782617-27782667	AG09319	gingival:	n/a
14	chr6:27782617-27782667	ECC-1	luminal epithelium:	n/a
15	chr6:27782617-27782667	GM12878	blood:	n/a
16	chr6:27782617-27782667	SK-N-SH_RA	brain:	n/a
17	chr6:27782617-27782667	HIPEpiC	eye:	n/a
18	chr6:27782617-27782667	NT2-D1	testis:	n/a
19	chr6:27782617-27782667	HUVEC	blood vessel:	n/a
20	chr6:27782617-27782667	ovcar-3	ovarian:	n/a
21	chr6:27782617-27782667	HepG2	liver:	n/a
22	chr6:27782617-27782667	CMK	blood:	n/a
23	chr6:27782617-27782667	BE2_C	brain:	n/a
24	chr6:27782617-27782667	HCF	heart:	n/a
25	chr6:27782617-27782667	LNCaP	prostate:	n/a
26	chr6:27782617-27782667	Jurkat	blood:	n/a
27	chr6:27782617-27782667	HPAEpiC	pulmonary alveolar:	n/a
28	chr6:27782617-27782667	AoSMC	blood vessel:	n/a
29	chr6:27782617-27782667	HAEpiC	amniotic membrane:	n/a
30	chr6:27782617-27782667	HMEC	breast:	n/a
31	chr6:27782617-27782667	GM12892	blood:	n/a
32	chr6:27782617-27782667	NHBE	bronchial:	n/a
33	chr6:27782617-27782667	HRE	kidney:	n/a
34	chr6:27782617-27782667	AG09309	skin:	n/a
35	chr6:27782617-27782667	H1-hESC	embryonic stem cell:	embryo
36	chr6:27782617-27782667	A549	lung:	n/a
37	chr6:27782617-27782667	GM12891	blood:	n/a
38	chr6:27782617-27782667	AG04449	skin:	fetal
39	chr6:27782617-27782667	PANC-1	pancreas:	n/a
40	chr6:27782617-27782667	U87	brain:	n/a
41	chr6:27782617-27782667	GM06990	blood:	n/a
42	chr6:27782617-27782667	PrEC	prostate:	n/a
43	chr6:27782617-27782667	IMR90	lung:	fetal
44	chr6:27782617-27782667	K562	blood:	n/a
45	chr6:27782617-27782667	SK-N-SH	brain:	n/a
46	chr6:27782617-27782667	HCPEpiC	choroid plexus:	n/a
47	chr6:27782617-27782667	HCT-116	colon:	n/a
48	chr6:27782617-27782667	HL-60	blood:	n/a
49	chr6:27782617-27782667	BJ	skin:	n/a
50	chr6:27782617-27782667	SAEC	small airway:	n/a

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26122455..26127911-chr6:27777953..27784057,9	MCF-7	breast:
2	chr6:27100161..27102247-chr6:27781053..27784459,3	MCF-7	breast:
3	chr6:26043139..26044932-chr6:27781664..27783621,2	MCF-7	breast:
4	chr6:27780572..27782800-chr6:28000600..28002491,2	K562	blood:
5	chr6:26182173..26185335-chr6:27780962..27783737,3	MCF-7	breast:
6	chr6:27780093..27783062-chr6:28322537..28324933,2	K562	blood:
7	chr6:26155301..26160613-chr6:27781458..27785146,6	MCF-7	breast:
8	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
9	chr1:185285853..185286793-chr6:27782269..27782920,2	Hela-S3	cervix:
10	chr6:27094403..27106138-chr6:27772392..27783072,46	MCF-7	breast:
11	chr6:26233018..26235518-chr6:27781228..27784528,3	MCF-7	breast:
12	chr6:27113704..27115641-chr6:27781150..27784385,3	MCF-7	breast:
13	chr6:27111360..27127716-chr6:27768319..27787545,69	MCF-7	breast:
14	chr6:26122193..26124669-chr6:27781205..27782892,3	MCF-7	breast:
15	chr19:46087794..46088378-chr6:27782398..27783153,2	Hela-S3	cervix:
16	chr6:27782015..27782992-chr8:95731280..95732018,2	NB4	blood:
17	chr6:26198554..26201743-chr6:27781165..27784293,4	MCF-7	breast:
18	chr14:64969586..64971373-chr6:27781788..27783642,2	MCF-7	breast:
19	chr6:26020260..26024010-chr6:27780504..27784636,5	MCF-7	breast:
20	chr6:27104887..27109324-chr6:27780147..27783327,4	MCF-7	breast:
21	chr17:39845026..39845560-chr6:27781945..27782733,2	Hela-S3	cervix:
22	chr2:183902933..183903582-chr6:27782215..27782898,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
HIST1H2BM	TF binding region
HIST1H2AJ	TF binding region
HIST1H2AJ	CpG island
HIST1H2BM	CpG island
ENSG00000173812	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000218281	Chromatin interaction
ENSG00000116679	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000234816	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000217315	Chromatin interaction
ENSG00000124575	Chromatin interaction
ENSG00000125741	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000196226	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000198366	Chromatin interaction
ENSG00000061676	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000196176	Chromatin interaction
ENSG00000089775	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000156162	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000197697	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
8	nsv970094	chr6:27782238-27786201	Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	41 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27774400-27784000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:27780200-27784000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:27780400-27783800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:27780800-27782800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:27780800-27784200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:27781000-27783000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:27781000-27783400	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr6:27781000-27784400	Active TSS	Brain Germinal Matrix	brain
9	chr6:27781200-27783600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:27781200-27783600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:27781200-27784000	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:27781200-27784400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr6:27781200-27784400	Active TSS	A549	lung
14	chr6:27781400-27782800	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr6:27781600-27782800	Active TSS	Fetal Muscle Trunk	muscle
16	chr6:27781600-27783000	Active TSS	Fetal Muscle Leg	muscle
17	chr6:27781600-27783200	Active TSS	Fetal Stomach	stomach
18	chr6:27781600-27783200	Active TSS	NH-A	brain
19	chr6:27781600-27783600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:27781600-27783600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:27781600-27783600	Active TSS	Fetal Brain Female	brain
22	chr6:27781600-27783800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:27781600-27784000	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr6:27781600-27784000	Active TSS	Thymus	Thymus
25	chr6:27781800-27782800	Active TSS	Muscle Satellite Cultured Cells	--
26	chr6:27781800-27782800	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr6:27781800-27782800	Active TSS	Rectal Smooth Muscle	rectum
28	chr6:27781800-27783000	Active TSS	Hela-S3	cervix
29	chr6:27781800-27783200	Active TSS	Fetal Kidney	kidney
30	chr6:27781800-27783200	Active TSS	HepG2	liver
31	chr6:27781800-27783400	Active TSS	HSMM	muscle
32	chr6:27781800-27783600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:27781800-27784000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:27781800-27784000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:27782000-27782800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:27782000-27782800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:27782000-27782800	Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr6:27782000-27782800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr6:27782000-27782800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:27782000-27782800	Active TSS	Colonic Mucosa	Colon
41	chr6:27782000-27782800	Active TSS	Fetal Thymus	thymus
42	chr6:27782000-27782800	Active TSS	HSMMtube	muscle
43	chr6:27782000-27783000	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr6:27782000-27783000	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr6:27782000-27783000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:27782000-27783000	Active TSS	Fetal Intestine Large	intestine
47	chr6:27782000-27783000	Active TSS	Placenta	Placenta
48	chr6:27782000-27783000	Active TSS	GM12878-XiMat	blood
49	chr6:27782000-27783200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:27782000-27783200	Active TSS	Breast Myoepithelial Primary Cells	Breast

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