Variant report

Variant	rs323897
Chromosome Location	chr3:52009612-52009613
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	POLR2A	chr3:52007740-52009785	Raji	blood:	n/a	n/a
2	MXI1	chr3:52008912-52010107	GM12878	blood:	n/a	chr3:52010037-52010052 chr3:52010035-52010050
3	MAX	chr3:52007479-52009764	ECC-1	luminal epithelium:	n/a	n/a
4	NRF1	chr3:52008564-52010272	SK-N-SH	brain:	n/a	chr3:52009076-52009087
5	MYC	chr3:52007633-52009752	K562	blood:	n/a	n/a
6	PML	chr3:52007585-52010148	GM12878	blood:	n/a	n/a
7	MAX	chr3:52007453-52009737	A549	lung:	n/a	n/a
8	ELF1	chr3:52008904-52009637	GM12878	blood:	n/a	n/a
9	MAX	chr3:52008819-52009774	SK-N-SH	brain:	n/a	n/a
10	MAX	chr3:52007541-52010195	ECC-1	luminal epithelium:	n/a	chr3:52010041-52010050
11	TFAP2A	chr3:52008976-52009776	Hela-S3	cervix:	n/a	chr3:52009294-52009305 chr3:52009296-52009304 chr3:52009294-52009305 chr3:52009290-52009305 chr3:52009296-52009304 chr3:52009295-52009303 chr3:52009294-52009305 chr3:52009295-52009303 chr3:52009296-52009304 chr3:52009227-52009238 chr3:52009294-52009305 chr3:52009295-52009303
12	POLR2A	chr3:52007231-52010021	HepG2	liver:	n/a	n/a
13	MAX	chr3:52007476-52009665	HepG2	liver:	n/a	n/a
14	MYC	chr3:52007626-52009697	NB4	blood:	n/a	n/a
15	POLR2A	chr3:52007578-52009690	MCF10A-Er-Src	breast:	n/a	n/a
16	MAX	chr3:52007638-52009721	NB4	blood:	n/a	n/a
17	MAX	chr3:52008920-52009753	MCF-7	breast:	n/a	n/a
18	MXI1	chr3:52008865-52009615	HepG2	liver:	n/a	n/a
19	MAX	chr3:52008826-52009656	GM12878	blood:	n/a	n/a
20	MXI1	chr3:52007385-52010519	SK-N-SH	brain:	n/a	chr3:52010037-52010052 chr3:52010035-52010050
21	TAF1	chr3:52008885-52009751	H1-neurons	neurons:	n/a	n/a
22	POLR2A	chr3:52008455-52009960	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr3:52008845-52009994	H1-neurons	neurons:	n/a	n/a
24	MTA3	chr3:52009329-52009878	GM12878	blood:	n/a	n/a
25	STAT1	chr3:52009564-52009734	GM12878	blood:	n/a	n/a
26	MYC	chr3:52009593-52009616	HUVEC	blood vessel:	n/a	n/a
27	MYC	chr3:52008889-52009681	Hela-S3	cervix:	n/a	n/a
28	MYC	chr3:52007481-52009692	K562	blood:	n/a	n/a
29	MAZ	chr3:52007409-52010418	IMR90	lung:	n/a	chr3:52010041-52010050
30	STAT5A	chr3:52007667-52010096	GM12878	blood:	n/a	chr3:52008697-52008709 chr3:52009473-52009485 chr3:52010059-52010071 chr3:52008703-52008715
31	BACH1	chr3:52008980-52009729	H1-hESC	embryonic stem cell:	n/a	n/a
32	RUNX3	chr3:52009398-52009935	GM12878	blood:	n/a	n/a
33	POLR2A	chr3:52008793-52009786	SK-N-SH	brain:	n/a	n/a
34	POU2F2	chr3:52008872-52009614	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:52007403-52009683	K562	blood:	n/a	n/a
36	POLR2A	chr3:52008895-52010314	H1-neurons	neurons:	n/a	n/a
37	REST	chr3:52008518-52010507	H1-neurons	neurons:	n/a	chr3:52008982-52008992 chr3:52008673-52008693 chr3:52009322-52009335
38	MTA3	chr3:52007442-52009848	GM12878	blood:	n/a	n/a
39	HCFC1	chr3:52007393-52009871	Hela-S3	cervix:	n/a	n/a
40	EP300	chr3:52009002-52009673	K562	blood:	n/a	n/a
41	MAX	chr3:52008886-52009642	A549	lung:	n/a	n/a
42	RUNX3	chr3:52009473-52010109	GM12878	blood:	n/a	n/a
43	ZKSCAN1	chr3:52009363-52009870	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:52007500-52009719	GM12891	blood:	n/a	n/a
45	MYC	chr3:52009609-52009636	HepG2	liver:	n/a	n/a
46	NFATC1	chr3:52009323-52009630	GM12878	blood:	n/a	n/a
47	YY1	chr3:52008723-52009616	SK-N-SH	brain:	n/a	chr3:52009089-52009101
48	CTCF	chr3:52009495-52010415	SK-N-SH	brain:	n/a	chr3:52010216-52010223
49	POLR2A	chr3:52007489-52009981	SK-N-MC	brain:	n/a	n/a
50	TFAP2C	chr3:52008928-52009791	Hela-S3	cervix:	n/a	chr3:52009293-52009308

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	chr3:51974179..51978718-chr3:52004198..52010829,11	K562	blood:

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

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11916396	1.00[ASN][1000 genomes]
rs11926611	0.84[YRI][hapmap]
rs188953	0.81[MKK][hapmap]
rs2015691	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs323858	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323859	0.84[AFR][1000 genomes]
rs323861	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323862	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323863	0.92[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs323865	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs323866	1.00[ASN][1000 genomes]
rs323867	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs323868	1.00[MEX][hapmap];0.84[MKK][hapmap]
rs323871	0.90[AMR][1000 genomes]
rs323873	1.00[MEX][hapmap];0.81[MKK][hapmap];0.90[AMR][1000 genomes]
rs323874	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs323879	1.00[MEX][hapmap];0.81[MKK][hapmap]
rs323887	1.00[MEX][hapmap]
rs323890	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323892	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs323893	0.84[YRI][hapmap]
rs323894	0.91[AFR][1000 genomes]
rs323895	0.84[YRI][hapmap]
rs323898	1.00[MEX][hapmap];0.84[MKK][hapmap]
rs379462	0.92[ASW][hapmap];1.00[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs380788	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs403620	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs404527	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs411209	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs433823	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs451154	0.84[AFR][1000 genomes]
rs72964028	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72964029	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7432986	0.92[ASW][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes]
rs82854	0.83[AFR][1000 genomes]
rs9840336	1.00[CHD][hapmap]

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	chr3:52007400-52009800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:52007400-52009800	Active TSS	Ovary	ovary
4	chr3:52007400-52010000	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr3:52007400-52010000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr3:52007400-52010000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr3:52007400-52010000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:52007400-52010000	Flanking Active TSS	Fetal Thymus	thymus
9	chr3:52007400-52010000	Flanking Active TSS	HMEC	breast
10	chr3:52007400-52010000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr3:52007400-52010200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr3:52007400-52010200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:52007400-52010400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr3:52007600-52010000	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr3:52007600-52010000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr3:52008000-52010000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:52008000-52010000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:52008000-52010400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:52008200-52010000	Flanking Active TSS	Colonic Mucosa	Colon
20	chr3:52008200-52010200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr3:52008200-52010200	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr3:52008200-52010400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:52008800-52009800	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr3:52008800-52010000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:52008800-52010200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:52008800-52010400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr3:52009000-52009800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:52009000-52009800	Active TSS	Fetal Brain Male	brain
29	chr3:52009000-52010400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:52009400-52009800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
31	chr3:52009400-52009800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:52009400-52009800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:52009400-52009800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
34	chr3:52009400-52009800	Flanking Active TSS	Esophagus	oesophagus
35	chr3:52009400-52009800	Flanking Active TSS	Fetal Brain Female	brain
36	chr3:52009400-52009800	Flanking Active TSS	Left Ventricle	heart
37	chr3:52009400-52009800	Flanking Active TSS	Pancreas	Pancrea
38	chr3:52009400-52009800	Flanking Active TSS	Hela-S3	cervix
39	chr3:52009400-52009800	Flanking Active TSS	HSMMtube	muscle
40	chr3:52009400-52009800	Flanking Active TSS	NHEK	skin
41	chr3:52009400-52010000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr3:52009400-52010000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:52009400-52010000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:52009400-52010000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:52009400-52010000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
46	chr3:52009400-52010000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:52009400-52010000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
48	chr3:52009400-52010000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
49	chr3:52009400-52010000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
50	chr3:52009400-52010000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

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