Variant report

Variant	rs323896
Chromosome Location	chr3:52008636-52008637
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:104)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:104 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52007740-52009785	Raji	blood:	n/a	n/a
2	RUNX3	chr3:52007485-52008703	GM12878	blood:	n/a	n/a
3	MAX	chr3:52008443-52008675	K562	blood:	n/a	n/a
4	MYBL2	chr3:52007824-52008661	HepG2	liver:	n/a	n/a
5	MAX	chr3:52007479-52009764	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr3:52008625-52008750	HepG2	liver:	n/a	n/a
7	CHD2	chr3:52007895-52009390	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:52008421-52009482	K562	blood:	n/a	n/a
9	MYC	chr3:52008541-52008653	MCF-7	breast:	n/a	n/a
10	YY1	chr3:52007552-52008767	HepG2	liver:	n/a	chr3:52008701-52008712
11	POLR2A	chr3:52007551-52009594	HepG2	liver:	n/a	n/a
12	NRF1	chr3:52008564-52010272	SK-N-SH	brain:	n/a	chr3:52009076-52009087
13	MYC	chr3:52007633-52009752	K562	blood:	n/a	n/a
14	POLR2A	chr3:52007591-52009513	MCF-7	breast:	n/a	n/a
15	POLR2A	chr3:52007621-52009533	HepG2	liver:	n/a	n/a
16	PML	chr3:52007585-52010148	GM12878	blood:	n/a	n/a
17	CHD2	chr3:52007768-52008899	K562	blood:	n/a	n/a
18	MAX	chr3:52007453-52009737	A549	lung:	n/a	n/a
19	POLR2A	chr3:52007735-52009470	HCT-116	colon:	n/a	n/a
20	POLR2A	chr3:52007611-52009359	HepG2	liver:	n/a	n/a
21	ZNF143	chr3:52007654-52008780	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr3:52007643-52009368	A549	lung:	n/a	chr3:52007771-52007784 chr3:52007774-52007783 chr3:52007769-52007787
23	POLR2A	chr3:52007733-52009526	K562	blood:	n/a	n/a
24	MAX	chr3:52007541-52010195	ECC-1	luminal epithelium:	n/a	chr3:52010041-52010050
25	HA-E2F1	chr3:52007629-52009570	MCF-7	breast:	n/a	chr3:52008979-52008994
26	POLR2A	chr3:52007231-52010021	HepG2	liver:	n/a	n/a
27	MAZ	chr3:52007670-52009475	K562	blood:	n/a	n/a
28	YY1	chr3:52008530-52008676	K562	blood:	n/a	n/a
29	POLR2A	chr3:52007545-52009469	HepG2	liver:	n/a	n/a
30	E2F6	chr3:52007465-52009450	H1-hESC	embryonic stem cell:	n/a	chr3:52008979-52008994
31	MAX	chr3:52007476-52009665	HepG2	liver:	n/a	n/a
32	CTCF	chr3:52008556-52008656	GM10266	blood:	n/a	n/a
33	POLR2A	chr3:52007662-52009525	GM18505	blood:	n/a	n/a
34	CTCF	chr3:52007954-52008667	GM12892	blood:	n/a	n/a
35	MYC	chr3:52007626-52009697	NB4	blood:	n/a	n/a
36	POLR2A	chr3:52007729-52009510	PBDE	blood:	n/a	n/a
37	POLR2A	chr3:52007578-52009690	MCF10A-Er-Src	breast:	n/a	n/a
38	MAX	chr3:52007638-52009721	NB4	blood:	n/a	n/a
39	POLR2A	chr3:52007502-52009428	Hela-S3	cervix:	n/a	n/a
40	EGR1	chr3:52008547-52008866	K562	blood:	n/a	chr3:52008696-52008709
41	SMARCC1	chr3:52007676-52008875	Hela-S3	cervix:	n/a	n/a
42	MXI1	chr3:52007385-52010519	SK-N-SH	brain:	n/a	chr3:52010037-52010052 chr3:52010035-52010050
43	E2F6	chr3:52007587-52009461	K562	blood:	n/a	chr3:52008979-52008994
44	NR2F2	chr3:52007488-52008916	K562	blood:	n/a	n/a
45	CTCF	chr3:52008580-52008730	GM06990	blood:	n/a	n/a
46	POLR2A	chr3:52008474-52008743	HepG2	liver:	n/a	n/a
47	POLR2A	chr3:52008455-52009960	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr3:52007642-52009517	GM19099	blood:	n/a	n/a
49	POLR2A	chr3:52008483-52008703	HCT-116	colon:	n/a	n/a
50	CTCF	chr3:52008500-52008650	HCM	heart:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52008016..52010191-chr3:52187253..52189980,2	MCF-7	breast:
2	chr3:51974812..51978768-chr3:52006594..52010604,6	MCF-7	breast:
3	chr3:52007628..52011282-chr3:52186808..52190381,5	K562	blood:
4	chr3:52005327..52011372-chr3:52027090..52031188,9	MCF-7	breast:
5	chr3:51974734..51977966-chr3:52006518..52010028,6	MCF-7	breast:
6	chr3:52006271..52012102-chr3:52024917..52032079,14	MCF-7	breast:
7	chr3:51974725..51977771-chr3:52005335..52009465,8	K562	blood:
8	chr3:51974179..51978718-chr3:52004198..52010829,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000254782	TF binding region
ENSG00000272762	TF binding region
ABHD14A	TF binding region
ABHD14A-ACY1	TF binding region
ABHD14B	TF binding region
ACY1	TF binding region
ENSG00000041880	Chromatin interaction
ENSG00000164087	Chromatin interaction
ENSG00000162244	Chromatin interaction
ENSG00000114767	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs178918	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323869	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323870	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323872	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323878	1.00[AMR][1000 genomes]
rs323880	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323889	1.00[AMR][1000 genomes]
rs323891	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs323900	1.00[AMR][1000 genomes]
rs368210	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs422304	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56746340	1.00[AMR][1000 genomes]
rs57384151	1.00[AMR][1000 genomes]
rs6446141	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72961930	1.00[AMR][1000 genomes]
rs72961999	1.00[AMR][1000 genomes]
rs72964016	1.00[AMR][1000 genomes]
rs7426999	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7636204	1.00[AMR][1000 genomes]
rs9683234	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv876781	chr3:51985664-52009612	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv876782	chr3:51985664-52022779	Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
12	nsv876783	chr3:51987224-52009612	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
13	nsv876784	chr3:51987224-52013242	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv876785	chr3:51994881-52022779	Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
15	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 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	chr3:52007200-52010200	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr3:52007400-52009000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:52007400-52009000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:52007400-52009000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
5	chr3:52007400-52009000	Flanking Active TSS	Primary B cells from peripheral blood	blood
6	chr3:52007400-52009000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
7	chr3:52007400-52009000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:52007400-52009000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:52007400-52009000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr3:52007400-52009000	Flanking Active TSS	Fetal Muscle Trunk	muscle
11	chr3:52007400-52009000	Flanking Active TSS	Fetal Muscle Leg	muscle
12	chr3:52007400-52009000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr3:52007400-52009000	Flanking Active TSS	Dnd41	blood
14	chr3:52007400-52009000	Flanking Active TSS	HUVEC	blood vessel
15	chr3:52007400-52009600	Active TSS	Psoas Muscle	Psoas
16	chr3:52007400-52009800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr3:52007400-52009800	Active TSS	Ovary	ovary
18	chr3:52007400-52010000	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr3:52007400-52010000	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr3:52007400-52010000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr3:52007400-52010000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:52007400-52010000	Flanking Active TSS	Fetal Thymus	thymus
23	chr3:52007400-52010000	Flanking Active TSS	HMEC	breast
24	chr3:52007400-52010000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr3:52007400-52010200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr3:52007400-52010200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:52007400-52010400	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr3:52007600-52008800	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr3:52007600-52009000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:52007600-52009000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:52007600-52009000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:52007600-52009000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:52007600-52009000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:52007600-52009000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:52007600-52009000	Flanking Active TSS	NH-A	brain
36	chr3:52007600-52009600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr3:52007600-52010000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr3:52007600-52010000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
39	chr3:52008000-52008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:52008000-52008800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:52008000-52008800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:52008000-52009000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52008000-52009000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:52008000-52009000	Flanking Active TSS	NHLF	lung
45	chr3:52008000-52010000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:52008000-52010000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr3:52008000-52010400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:52008200-52008800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr3:52008200-52008800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:52008200-52008800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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