Variant report

Variant	rs398123460
Chromosome Location	chr3:135969401-135969402
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:423)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:423 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

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	chr3:135968991-135969606	GM12878	blood:	n/a	chr3:135969505-135969518 chr3:135969187-135969203
8	RCOR1	chr3:135968845-135970213	K562	blood:	n/a	n/a
9	MAZ	chr3:135968940-135969759	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr3:135969340-135969554	Spleen_OC	spleen:	n/a	chr3:135969505-135969518
11	TCF12	chr3:135969019-135969477	H1-hESC	embryonic stem cell:	n/a	n/a
12	GTF2F1	chr3:135968853-135970150	K562	blood:	n/a	n/a
13	MAX	chr3:135968901-135970258	SK-N-SH	brain:	n/a	chr3:135969975-135969985
14	POLR2A	chr3:135968937-135969439	K562	blood:	n/a	n/a
15	POLR2A	chr3:135968640-135970593	GM12878	blood:	n/a	n/a
16	MYC	chr3:135968702-135970404	K562	blood:	n/a	chr3:135969975-135969985
17	MAX	chr3:135969029-135970302	K562	blood:	n/a	chr3:135969975-135969985
18	CHD2	chr3:135968895-135970290	GM12878	blood:	n/a	n/a
19	HCFC1	chr3:135968899-135970307	K562	blood:	n/a	n/a
20	TBL1XR1	chr3:135968897-135970450	K562	blood:	n/a	n/a
21	REST	chr3:135968987-135969524	A549	lung:	n/a	chr3:135969050-135969063 chr3:135969047-135969060
22	POLR2A	chr3:135968842-135970657	K562	blood:	n/a	n/a
23	NFIC	chr3:135968698-135970035	HepG2	liver:	n/a	n/a
24	RUNX3	chr3:135968822-135970578	GM12878	blood:	n/a	n/a
25	GTF3C2	chr3:135968625-135969440	K562	blood:	n/a	n/a
26	RFX5	chr3:135969021-135969635	GM12878	blood:	n/a	n/a
27	RAD21	chr3:135968939-135969706	H1-hESC	embryonic stem cell:	n/a	chr3:135969130-135969144 chr3:135969504-135969518
28	POLR2A	chr3:135968899-135970272	K562	blood:	n/a	n/a
29	FOXA1	chr3:135968995-135969639	T-47D	breast:	n/a	n/a
30	MAFF	chr3:135968799-135969678	HepG2	liver:	n/a	chr3:135969202-135969220
31	HA-E2F1	chr3:135968870-135969816	MCF-7	breast:	n/a	chr3:135969143-135969152 chr3:135969108-135969118
32	MYC	chr3:135968910-135970099	H1-hESC	embryonic stem cell:	n/a	chr3:135969975-135969985
33	HCFC1	chr3:135968361-135970554	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:135969077-135969672	HepG2	liver:	n/a	n/a
35	TCF7L2	chr3:135969007-135969596	HCT-116	colon:	n/a	n/a
36	E2F6	chr3:135968981-135969625	H1-hESC	embryonic stem cell:	n/a	chr3:135969143-135969152 chr3:135969108-135969118
37	POLR2A	chr3:135968497-135970273	Raji	blood:	n/a	n/a
38	POLR2A	chr3:135968917-135969638	MCF-7	breast:	n/a	n/a
39	CTCF	chr3:135969023-135969514	K562	blood:	n/a	chr3:135969187-135969203
40	TCF7L2	chr3:135968902-135970203	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr3:135968891-135970376	GM12878	blood:	n/a	n/a
42	CREB1	chr3:135969055-135969603	ECC-1	luminal epithelium:	n/a	n/a
43	MTA3	chr3:135968669-135969505	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:135968738-135969625	GM10847	blood:	n/a	n/a
45	FOS	chr3:135969334-135969430	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr3:135968798-135970334	H1-hESC	embryonic stem cell:	n/a	n/a
47	NRF1	chr3:135968950-135969549	Hela-S3	cervix:	n/a	chr3:135969142-135969153 chr3:135969139-135969153 chr3:135969142-135969151 chr3:135969167-135969178 chr3:135969141-135969152
48	POLR2A	chr3:135968913-135970034	MCF10A-Er-Src	breast:	n/a	n/a
49	UBTF	chr3:135968861-135969545	K562	blood:	n/a	n/a
50	ETS1	chr3:135968999-135969415	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:135969387-135969437	A549	lung:	n/a
2	chr3:135969387-135969437	U87	brain:	n/a
3	chr3:135969387-135969437	GM12891	blood:	n/a
4	chr3:135969387-135969437	T-47D	breast:	n/a
5	chr3:135969387-135969437	MCF-7	breast:	n/a
6	chr3:135969387-135969437	AoSMC	blood vessel:	n/a
7	chr3:135969387-135969437	AG09319	gingival:	n/a
8	chr3:135969387-135969437	HAEpiC	amniotic membrane:	n/a
9	chr3:135969387-135969437	NH-A	brain:	n/a
10	chr3:135969387-135969437	HUVEC	blood vessel:	n/a
11	chr3:135969387-135969437	AG09309	skin:	n/a
12	chr3:135969387-135969437	GM19239	blood:	n/a
13	chr3:135969387-135969437	SK-N-SH	brain:	n/a
14	chr3:135969387-135969437	HEEpiC	esophagus:	n/a
15	chr3:135969387-135969437	H1-hESC	embryonic stem cell:	embryo
16	chr3:135969387-135969437	SAEC	small airway:	n/a
17	chr3:135969387-135969437	HNPCEpiC	eye:	n/a
18	chr3:135969387-135969437	BE2_C	brain:	n/a
19	chr3:135969387-135969437	AG10803	skin:	n/a
20	chr3:135969387-135969437	HCPEpiC	choroid plexus:	n/a
21	chr3:135969387-135969437	NHBE	bronchial:	n/a
22	chr3:135969387-135969437	K562	blood:	n/a
23	chr3:135969387-135969437	HRE	kidney:	n/a
24	chr3:135969387-135969437	ECC-1	luminal epithelium:	n/a
25	chr3:135969387-135969437	RPTEC	kidney:	n/a
26	chr3:135969387-135969437	SKMC	muscle:	n/a
27	chr3:135969387-135969437	HL-60	blood:	n/a
28	chr3:135969387-135969437	HIPEpiC	eye:	n/a
29	chr3:135969387-135969437	NHDF-neo	bronchial:	n/a
30	chr3:135969387-135969437	GM12878	blood:	n/a
31	chr3:135969387-135969437	IMR90	lung:	fetal
32	chr3:135969387-135969437	PFSK-1	brain:	n/a
33	chr3:135969387-135969437	GM12892	blood:	n/a
34	chr3:135969387-135969437	AG04450	lung:	fetal
35	chr3:135969387-135969437	HMEC	breast:	n/a
36	chr3:135969387-135969437	HRPEpiC	eye:	n/a
37	chr3:135969387-135969437	Jurkat	blood:	n/a
38	chr3:135969387-135969437	HPAEpiC	pulmonary alveolar:	n/a
39	chr3:135969387-135969437	Caco-2	colon:	n/a
40	chr3:135969387-135969437	LNCaP	prostate:	n/a
41	chr3:135969387-135969437	HRCEpiC	kidney:	n/a
42	chr3:135969387-135969437	MCF10A-Er-Src	breast:	n/a
43	chr3:135969387-135969437	HEK293	kidney:	embryo
44	chr3:135969387-135969437	BJ	skin:	n/a
45	chr3:135969387-135969437	ovcar-3	ovarian:	n/a
46	chr3:135969387-135969437	HepG2	liver:	n/a
47	chr3:135969387-135969437	PANC-1	pancreas:	n/a
48	chr3:135969387-135969437	HCT-116	colon:	n/a
49	chr3:135969387-135969437	ProgFib	skin:	n/a
50	chr3:135969387-135969437	HCM	heart:	n/a

(count:14 , 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	chr11:10830178..10831145-chr3:135969170..135969695,2	Hela-S3	cervix:
8	chr3:135969104..135971090-chr3:136470031..136473091,3	MCF-7	breast:
9	chr3:135912523..135919453-chr3:135966949..135972062,29	K562	blood:
10	chr3:135914645..135915534-chr3:135968907..135969695,2	Hela-S3	cervix:
11	chr3:135912324..135920790-chr3:135965276..135971841,24	K562	blood:
12	chr3:135913275..135917052-chr3:135966241..135970685,15	MCF-7	breast:
13	chr3:135967505..135970256-chr3:136469769..136472442,3	K562	blood:
14	chr3:135914832..135915585-chr3:135969132..135969693,2	MCF-7	breast:

No data

Variant related genes	Relation type
PCCB	TF binding region
PCCB	CpG island
ENSG00000174579	Chromatin interaction
ENSG00000246308	Chromatin interaction
ENSG00000118007	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000261758	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000114054	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	chr3:135968600-135969600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:135968600-135969600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:135968600-135969600	Active TSS	Brain Germinal Matrix	brain
4	chr3:135968600-135969600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr3:135968600-135969800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:135968600-135969800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:135968600-135969800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr3:135968600-135969800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr3:135968600-135969800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:135968600-135969800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:135968600-135969800	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr3:135968600-135969800	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr3:135968600-135969800	Active TSS	Brain Anterior Caudate	brain
14	chr3:135968600-135969800	Active TSS	Fetal Brain Female	brain
15	chr3:135968600-135969800	Active TSS	Fetal Intestine Large	intestine
16	chr3:135968600-135969800	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr3:135968600-135969800	Enhancers	Spleen	Spleen
18	chr3:135968600-135970000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:135968600-135970200	Active TSS	Fetal Lung	lung
20	chr3:135968600-135970200	Active TSS	Rectal Smooth Muscle	rectum
21	chr3:135968600-135970400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr3:135968600-135970400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr3:135968800-135969600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:135968800-135969600	Active TSS	Primary T cells from cord blood	blood
25	chr3:135968800-135969600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:135968800-135969600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr3:135968800-135969600	Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr3:135968800-135969600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr3:135968800-135969600	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr3:135968800-135969600	Active TSS	Adipose Nuclei	Adipose
31	chr3:135968800-135969600	Active TSS	Fetal Heart	heart
32	chr3:135968800-135969600	Active TSS	Stomach Mucosa	stomach
33	chr3:135968800-135969600	Active TSS	HMEC	breast
34	chr3:135968800-135969600	Active TSS	HSMMtube	muscle
35	chr3:135968800-135969600	Active TSS	NH-A	brain
36	chr3:135968800-135969800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:135968800-135969800	Active TSS	H9 Cell Line	embryonic stem cell
38	chr3:135968800-135969800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:135968800-135969800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:135968800-135969800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:135968800-135969800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:135968800-135969800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:135968800-135969800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:135968800-135969800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:135968800-135969800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:135968800-135969800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:135968800-135969800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:135968800-135969800	Active TSS	Colonic Mucosa	Colon
49	chr3:135968800-135969800	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr3:135968800-135969800	Active TSS	Esophagus	oesophagus

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