Variant report

Variant	rs323890
Chromosome Location	chr3:52016337-52016338
allele	C/T
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	HNF4G	chr3:52016240-52016931	HepG2	liver:	n/a	chr3:52016602-52016610 chr3:52016594-52016616 chr3:52016598-52016612 chr3:52016917-52016929 chr3:52016599-52016611 chr3:52016422-52016437 chr3:52016596-52016611 chr3:52016598-52016612
2	CTCF	chr3:52016220-52016370	GM12873	blood:	n/a	n/a
3	E2F6	chr3:52016310-52017832	H1-hESC	embryonic stem cell:	n/a	n/a
4	MXI1	chr3:52016186-52018259	SK-N-SH	brain:	n/a	n/a
5	MYBL2	chr3:52016223-52017945	HepG2	liver:	n/a	n/a
6	FOSL2	chr3:52016312-52016783	A549	lung:	n/a	chr3:52016559-52016570 chr3:52016559-52016569
7	MAX	chr3:52016254-52017871	A549	lung:	n/a	chr3:52016849-52016860 chr3:52016846-52016861
8	TCF12	chr3:52016306-52017761	A549	lung:	n/a	chr3:52016606-52016616
9	MYC	chr3:52016253-52017809	A549	lung:	n/a	chr3:52016849-52016860 chr3:52016846-52016861
10	SP1	chr3:52016307-52016922	HepG2	liver:	n/a	n/a
11	TCF12	chr3:52016323-52017796	ECC-1	luminal epithelium:	n/a	chr3:52016606-52016616
12	CTCF	chr3:52016291-52017184	HCT-116	colon:	n/a	chr3:52016687-52016696
13	MTA3	chr3:52016241-52017786	GM12878	blood:	n/a	n/a
14	HCFC1	chr3:52016206-52018313	Hela-S3	cervix:	n/a	n/a
15	MAZ	chr3:52016114-52017957	IMR90	lung:	n/a	chr3:52016849-52016860 chr3:52016846-52016861
16	MAFF	chr3:52016239-52016780	HepG2	liver:	n/a	n/a
17	MAX	chr3:52016318-52017880	HCT-116	colon:	n/a	chr3:52016849-52016860 chr3:52016846-52016861
18	MYC	chr3:52016278-52017718	MCF10A-Er-Src	breast:	n/a	chr3:52016849-52016860 chr3:52016846-52016861
19	CTCF	chr3:52016257-52017799	A549	lung:	n/a	chr3:52016687-52016696
20	HEY1	chr3:52016297-52018485	HepG2	liver:	n/a	chr3:52016758-52016767
21	CREB1	chr3:52016266-52018413	HepG2	liver:	n/a	chr3:52016755-52016768
22	MYBL2	chr3:52016160-52017051	HepG2	liver:	n/a	n/a
23	JUN	chr3:52016249-52017898	K562	blood:	n/a	chr3:52016559-52016569
24	MAX	chr3:52016212-52017851	HCT-116	colon:	n/a	chr3:52016849-52016860 chr3:52016846-52016861
25	POLR2A	chr3:52016315-52017088	HepG2	liver:	n/a	n/a
26	MAX	chr3:52016251-52018418	HepG2	liver:	n/a	chr3:52016849-52016860 chr3:52016846-52016861
27	CTCF	chr3:52016208-52017431	HCT-116	colon:	n/a	chr3:52016687-52016696
28	MBD4	chr3:52016297-52016983	HepG2	liver:	n/a	n/a
29	POLR2A	chr3:52016082-52030443	HepG2	liver:	n/a	n/a
30	FOSL2	chr3:52016264-52016851	HepG2	liver:	n/a	chr3:52016559-52016570 chr3:52016559-52016569
31	MAZ	chr3:52016291-52017814	GM12878	blood:	n/a	chr3:52016849-52016860 chr3:52016846-52016861
32	ARID3A	chr3:52016298-52016899	HepG2	liver:	n/a	n/a
33	FOSL2	chr3:52016304-52016895	HepG2	liver:	n/a	chr3:52016559-52016570 chr3:52016559-52016569
34	POLR2A	chr3:52016306-52018700	HepG2	liver:	n/a	n/a
35	CTCF	chr3:52016300-52017799	SK-N-SH	brain:	n/a	chr3:52016687-52016696
36	TEAD4	chr3:52016259-52017344	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52015341..52017883-chr3:52186866..52188474,2	MCF-7	breast:
2	chr3:52015921..52019600-chr3:52088214..52092499,4	K562	blood:
3	chr3:52015955..52017820-chr3:52311212..52313632,2	K562	blood:
4	chr3:52016320..52018909-chr3:52089400..52091632,2	MCF-7	breast:
5	chr3:51975062..51978431-chr3:52015984..52020263,5	K562	blood:
6	chr3:52015943..52018006-chr3:52443224..52445803,2	K562	blood:
7	chr3:52014600..52016673-chr3:52222522..52224702,2	K562	blood:
8	chr3:51975879..51978347-chr3:52015319..52018171,3	MCF-7	breast:
9	chr3:51974624..51978885-chr3:52015984..52028227,23	K562	blood:

Variant related genes	Relation type
ACY1	TF binding region
ENSG00000164086	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000010318	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000114767	Chromatin interaction
ENSG00000164087	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11916396	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2015691	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323858	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323859	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs323861	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323862	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323865	1.00[ASN][1000 genomes]
rs323866	1.00[ASN][1000 genomes]
rs323867	1.00[ASN][1000 genomes]
rs323868	0.90[AMR][1000 genomes]
rs323879	0.90[AMR][1000 genomes]
rs323892	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323894	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs323897	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs379462	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs380788	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs403620	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs404527	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	0.96[AFR][1000 genomes]
rs433823	1.00[ASN][1000 genomes]
rs451154	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs72964028	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72964029	1.00[ASN][1000 genomes]
rs82854	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
11	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
12	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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52009800-52016400	Weak transcription	Small Intestine	intestine
2	chr3:52010000-52016400	Weak transcription	Left Ventricle	heart
3	chr3:52010000-52016400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:52010000-52016400	Weak transcription	Psoas Muscle	Psoas
5	chr3:52010000-52016400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:52010000-52016400	Weak transcription	HSMMtube	muscle
7	chr3:52010000-52016400	Weak transcription	NHDF-Ad	bronchial
8	chr3:52010200-52016400	Weak transcription	HSMM	muscle
9	chr3:52010200-52016400	Weak transcription	NH-A	brain
10	chr3:52010200-52016600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:52010400-52016400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:52010400-52016400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:52010400-52016400	Weak transcription	Brain Anterior Caudate	brain
14	chr3:52010400-52016400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:52010600-52016400	Weak transcription	Fetal Brain Male	brain
16	chr3:52011800-52016400	Weak transcription	Fetal Thymus	thymus
17	chr3:52012400-52016400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:52012400-52016400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:52012600-52016400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:52012600-52016400	Weak transcription	NHEK	skin
21	chr3:52013200-52016400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:52014200-52016400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:52014400-52016600	Enhancers	Pancreas	Pancrea
24	chr3:52014400-52016600	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr3:52014600-52016400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr3:52014800-52016400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:52014800-52016400	Enhancers	Stomach Mucosa	stomach
28	chr3:52015000-52016400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:52015200-52016400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:52015200-52016400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:52015200-52016400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:52015200-52016400	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:52015200-52016400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:52015200-52016400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr3:52015200-52016400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:52015200-52016400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:52015200-52016400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:52015200-52016400	Weak transcription	Esophagus	oesophagus
39	chr3:52015200-52016400	Weak transcription	Right Atrium	heart
40	chr3:52015200-52016400	Enhancers	Right Ventricle	heart
41	chr3:52015200-52016400	Weak transcription	Thymus	Thymus
42	chr3:52015400-52016400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52015400-52016400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:52015400-52016400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr3:52015400-52016400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:52015400-52016400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:52015400-52016400	Enhancers	Adipose Nuclei	Adipose
48	chr3:52015400-52016400	Weak transcription	Brain Angular Gyrus	brain
49	chr3:52015400-52016400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr3:52015400-52016400	Enhancers	Skeletal Muscle Male	skeletal muscle

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