Variant report

Variant	rs546682085
Chromosome Location	chr3:135969160-135969161
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:567)
CpG islands
(count:122)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:567 , 50 per page) page: 1 2 3 4 5 6 7 ... 12

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr3:135969038-135969657	HepG2	liver:	n/a	chr3:135969425-135969434 chr3:135969424-135969436
2	MXI1	chr3:135968877-135969985	Hela-S3	cervix:	n/a	n/a
3	TCF3	chr3:135969109-135969430	GM12878	blood:	n/a	n/a
4	PAX5	chr3:135968998-135969432	GM12878	blood:	n/a	chr3:135969006-135969024
5	MXI1	chr3:135968554-135970729	SK-N-SH	brain:	n/a	n/a
6	TCF3	chr3:135969032-135969562	GM12878	blood:	n/a	n/a
7	CTCF	chr3:135969120-135969270	HCM	heart:	n/a	chr3:135969187-135969203
8	CTCF	chr3:135968991-135969606	GM12878	blood:	n/a	chr3:135969505-135969518 chr3:135969187-135969203
9	RCOR1	chr3:135968845-135970213	K562	blood:	n/a	n/a
10	MAZ	chr3:135968940-135969759	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr3:135969140-135969290	GM12874	blood:	n/a	chr3:135969187-135969203
12	TCF12	chr3:135969019-135969477	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr3:135969080-135969230	HPAF	blood vessel:	n/a	chr3:135969187-135969203
14	GTF2F1	chr3:135968853-135970150	K562	blood:	n/a	n/a
15	CBX3	chr3:135969000-135969321	K562	blood:	n/a	n/a
16	MAX	chr3:135968901-135970258	SK-N-SH	brain:	n/a	chr3:135969975-135969985
17	POLR2A	chr3:135968937-135969439	K562	blood:	n/a	n/a
18	POLR2A	chr3:135968640-135970593	GM12878	blood:	n/a	n/a
19	MYC	chr3:135968702-135970404	K562	blood:	n/a	chr3:135969975-135969985
20	CTCF	chr3:135969080-135969230	A549	lung:	n/a	chr3:135969187-135969203
21	CTCF	chr3:135969100-135969250	GM12872	blood:	n/a	chr3:135969187-135969203
22	MAX	chr3:135969029-135970302	K562	blood:	n/a	chr3:135969975-135969985
23	CTCF	chr3:135969080-135969230	HVMF	connective:	n/a	chr3:135969187-135969203
24	CHD2	chr3:135968895-135970290	GM12878	blood:	n/a	n/a
25	HCFC1	chr3:135968899-135970307	K562	blood:	n/a	n/a
26	TBL1XR1	chr3:135968897-135970450	K562	blood:	n/a	n/a
27	REST	chr3:135968987-135969524	A549	lung:	n/a	chr3:135969050-135969063 chr3:135969047-135969060
28	POLR2A	chr3:135968842-135970657	K562	blood:	n/a	n/a
29	NFIC	chr3:135968698-135970035	HepG2	liver:	n/a	n/a
30	RUNX3	chr3:135968822-135970578	GM12878	blood:	n/a	n/a
31	CTCF	chr3:135969140-135969290	AG04450	lung:	n/a	chr3:135969187-135969203
32	GTF3C2	chr3:135968625-135969440	K562	blood:	n/a	n/a
33	RFX5	chr3:135969021-135969635	GM12878	blood:	n/a	n/a
34	RAD21	chr3:135968939-135969706	H1-hESC	embryonic stem cell:	n/a	chr3:135969130-135969144 chr3:135969504-135969518
35	POLR2A	chr3:135968899-135970272	K562	blood:	n/a	n/a
36	CTCF	chr3:135969100-135969250	Hela-S3	cervix:	n/a	chr3:135969187-135969203
37	FOXA1	chr3:135968995-135969639	T-47D	breast:	n/a	n/a
38	CTCF	chr3:135969100-135969250	HCFaa	heart:	n/a	chr3:135969187-135969203
39	MAFF	chr3:135968799-135969678	HepG2	liver:	n/a	chr3:135969202-135969220
40	HA-E2F1	chr3:135968870-135969816	MCF-7	breast:	n/a	chr3:135969143-135969152 chr3:135969108-135969118
41	MYC	chr3:135968910-135970099	H1-hESC	embryonic stem cell:	n/a	chr3:135969975-135969985
42	CTCF	chr3:135969140-135969290	HRPEpiC	eye:	n/a	chr3:135969187-135969203
43	HCFC1	chr3:135968361-135970554	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:135969077-135969672	HepG2	liver:	n/a	n/a
45	TCF7L2	chr3:135969007-135969596	HCT-116	colon:	n/a	n/a
46	E2F6	chr3:135968981-135969625	H1-hESC	embryonic stem cell:	n/a	chr3:135969143-135969152 chr3:135969108-135969118
47	POLR2A	chr3:135968497-135970273	Raji	blood:	n/a	n/a
48	POLR2A	chr3:135968917-135969638	MCF-7	breast:	n/a	n/a
49	CTCF	chr3:135969023-135969514	K562	blood:	n/a	chr3:135969187-135969203
50	TCF7L2	chr3:135968902-135970203	Hela-S3	cervix:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:135969136-135969186	NT2-D1	testis:	n/a
2	chr3:135969116-135969166	HEK293	kidney:	embryo
3	chr3:135969136-135969186	HAEpiC	amniotic membrane:	n/a
4	chr3:135969136-135969186	Hela-S3	cervix:	n/a
5	chr3:135969116-135969166	HCM	heart:	n/a
6	chr3:135969116-135969166	RPTEC	kidney:	n/a
7	chr3:135969136-135969186	PFSK-1	brain:	n/a
8	chr3:135969116-135969166	HNPCEpiC	eye:	n/a
9	chr3:135969136-135969186	AoSMC	blood vessel:	n/a
10	chr3:135969136-135969186	HRE	kidney:	n/a
11	chr3:135969116-135969166	HRE	kidney:	n/a
12	chr3:135969136-135969186	SK-N-SH_RA	brain:	n/a
13	chr3:135969136-135969186	HUVEC	blood vessel:	n/a
14	chr3:135969136-135969186	GM19239	blood:	n/a
15	chr3:135969116-135969166	AG04450	lung:	fetal
16	chr3:135969136-135969186	HCM	heart:	n/a
17	chr3:135969116-135969166	Hela-S3	cervix:	n/a
18	chr3:135969136-135969186	SAEC	small airway:	n/a
19	chr3:135969136-135969186	A549	lung:	n/a
20	chr3:135969116-135969166	GM12892	blood:	n/a
21	chr3:135969116-135969166	HAEpiC	amniotic membrane:	n/a
22	chr3:135969116-135969166	GM19239	blood:	n/a
23	chr3:135969136-135969186	HPAEpiC	pulmonary alveolar:	n/a
24	chr3:135969136-135969186	Hepatocyte	liver:	n/a
25	chr3:135969116-135969166	Jurkat	blood:	n/a
26	chr3:135969116-135969166	HL-60	blood:	n/a
27	chr3:135969116-135969166	GM06990	blood:	n/a
28	chr3:135969116-135969166	NHBE	bronchial:	n/a
29	chr3:135969116-135969166	CMK	blood:	n/a
30	chr3:135969116-135969166	ECC-1	luminal epithelium:	n/a
31	chr3:135969116-135969166	H1-hESC	embryonic stem cell:	embryo
32	chr3:135969136-135969186	HRPEpiC	eye:	n/a
33	chr3:135969136-135969186	GM06990	blood:	n/a
34	chr3:135969116-135969166	PANC-1	pancreas:	n/a
35	chr3:135969136-135969186	HIPEpiC	eye:	n/a
36	chr3:135969136-135969186	CMK	blood:	n/a
37	chr3:135969136-135969186	HMEC	breast:	n/a
38	chr3:135969136-135969186	NHDF-neo	bronchial:	n/a
39	chr3:135969116-135969166	NB4	blood:	n/a
40	chr3:135969116-135969166	Caco-2	colon:	n/a
41	chr3:135969136-135969186	SK-N-MC	brain:	n/a
42	chr3:135969116-135969166	HCPEpiC	choroid plexus:	n/a
43	chr3:135969136-135969186	BJ	skin:	n/a
44	chr3:135969116-135969166	BJ	skin:	n/a
45	chr3:135969116-135969166	K562	blood:	n/a
46	chr3:135969116-135969166	PrEC	prostate:	n/a
47	chr3:135969116-135969166	NH-A	brain:	n/a
48	chr3:135969136-135969186	AG04450	lung:	fetal
49	chr3:135969136-135969186	GM12892	blood:	n/a
50	chr3:135969136-135969186	T-47D	breast:	n/a

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:135968568..135972532-chr3:135974380..135977728,5	K562	blood:
2	chr3:135967895..135971293-chr3:135973278..135977937,5	MCF-7	breast:
3	chr3:135968947..135969500-chr6:27100458..27101422,2	HCT-116	colon:
4	chr3:135912206..135917353-chr3:135967047..135972220,20	MCF-7	breast:
5	chr3:135968756..135970580-chr3:136469634..136471998,2	K562	blood:
6	chr3:135968107..135969967-chr3:136470513..136472370,2	MCF-7	breast:
7	chr3:135969104..135971090-chr3:136470031..136473091,3	MCF-7	breast:
8	chr3:135912523..135919453-chr3:135966949..135972062,29	K562	blood:
9	chr3:135914645..135915534-chr3:135968907..135969695,2	Hela-S3	cervix:
10	chr3:135912324..135920790-chr3:135965276..135971841,24	K562	blood:
11	chr3:135913275..135917052-chr3:135966241..135970685,15	MCF-7	breast:
12	chr3:135967505..135970256-chr3:136469769..136472442,3	K562	blood:
13	chr3:135914832..135915585-chr3:135969132..135969693,2	MCF-7	breast:

No data

Variant related genes	Relation type
PCCB	TF binding region
PCCB	CpG island
ENSG00000124635	Chromatin interaction
ENSG00000114054	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv508246	chr3:135922023-136038622	Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv933522	chr3:135968919-135981180	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135968600-135969200	Flanking Active TSS	Fetal Muscle Trunk	muscle
2	chr3:135968600-135969200	Flanking Active TSS	Dnd41	blood
3	chr3:135968600-135969400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:135968600-135969600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:135968600-135969600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:135968600-135969600	Active TSS	Brain Germinal Matrix	brain
7	chr3:135968600-135969600	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr3:135968600-135969800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:135968600-135969800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:135968600-135969800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:135968600-135969800	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr3:135968600-135969800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr3:135968600-135969800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:135968600-135969800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:135968600-135969800	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr3:135968600-135969800	Active TSS	Brain Anterior Caudate	brain
17	chr3:135968600-135969800	Active TSS	Fetal Brain Female	brain
18	chr3:135968600-135969800	Active TSS	Fetal Intestine Large	intestine
19	chr3:135968600-135969800	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr3:135968600-135969800	Enhancers	Spleen	Spleen
21	chr3:135968600-135970000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:135968600-135970200	Active TSS	Fetal Lung	lung
23	chr3:135968600-135970200	Active TSS	Rectal Smooth Muscle	rectum
24	chr3:135968600-135970400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr3:135968600-135970400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr3:135968800-135969200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr3:135968800-135969200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr3:135968800-135969200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr3:135968800-135969200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:135968800-135969200	Flanking Active TSS	Fetal Brain Male	brain
31	chr3:135968800-135969200	Flanking Active TSS	Placenta	Placenta
32	chr3:135968800-135969200	Flanking Active TSS	Fetal Thymus	thymus
33	chr3:135968800-135969200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr3:135968800-135969200	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr3:135968800-135969200	Flanking Active TSS	Thymus	Thymus
36	chr3:135968800-135969600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:135968800-135969600	Active TSS	Primary T cells from cord blood	blood
38	chr3:135968800-135969600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:135968800-135969600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:135968800-135969600	Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr3:135968800-135969600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr3:135968800-135969600	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr3:135968800-135969600	Active TSS	Adipose Nuclei	Adipose
44	chr3:135968800-135969600	Active TSS	Fetal Heart	heart
45	chr3:135968800-135969600	Active TSS	Stomach Mucosa	stomach
46	chr3:135968800-135969600	Active TSS	HMEC	breast
47	chr3:135968800-135969600	Active TSS	HSMMtube	muscle
48	chr3:135968800-135969600	Active TSS	NH-A	brain
49	chr3:135968800-135969800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:135968800-135969800	Active TSS	H9 Cell Line	embryonic stem cell

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