Variant report

Variant	rs3803456
Chromosome Location	chr15:57210136-57210137
allele	A/G
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	chr15:57209696-57212423	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr15:57209841-57210747	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr15:57210120-57211157	ECC-1	luminal epithelium:	n/a	chr15:57210744-57210754
4	CUX1	chr15:57210087-57210426	K562	blood:	n/a	n/a
5	POLR2A	chr15:57209256-57213061	MCF10A-Er-Src	breast:	n/a	n/a
6	TAF1	chr15:57210021-57212293	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUN	chr15:57209836-57213020	K562	blood:	n/a	chr15:57211660-57211671 chr15:57211663-57211673 chr15:57212474-57212482 chr15:57211663-57211673 chr15:57212472-57212484 chr15:57211663-57211673 chr15:57212473-57212483
8	MAX	chr15:57209944-57211084	K562	blood:	n/a	chr15:57210744-57210754
9	MYC	chr15:57209765-57211087	K562	blood:	n/a	chr15:57210744-57210754
10	MAZ	chr15:57210136-57211848	GM12878	blood:	n/a	chr15:57210744-57210754
11	E2F6	chr15:57209826-57211149	H1-hESC	embryonic stem cell:	n/a	chr15:57210776-57210785 chr15:57210743-57210752 chr15:57211095-57211105 chr15:57210740-57210752
12	TAL1	chr15:57210128-57210136	K562	blood:	n/a	n/a
13	RELA	chr15:57210120-57210995	GM18951	blood:	n/a	n/a
14	HCFC1	chr15:57210031-57213492	Hela-S3	cervix:	n/a	n/a
15	TCF12	chr15:57210064-57211173	ECC-1	luminal epithelium:	n/a	chr15:57211095-57211105
16	MAX	chr15:57209993-57211003	A549	lung:	n/a	chr15:57210744-57210754
17	MTA3	chr15:57209958-57211028	GM12878	blood:	n/a	n/a
18	SIX5	chr15:57210060-57211210	A549	lung:	n/a	n/a
19	MAZ	chr15:57209943-57212243	IMR90	lung:	n/a	chr15:57210744-57210754
20	PBX3	chr15:57209834-57211194	A549	lung:	n/a	n/a
21	POLR2A	chr15:57209944-57212530	HUVEC	blood vessel:	n/a	n/a
22	YY1	chr15:57209718-57211626	GM12891	blood:	n/a	chr15:57209903-57209915 chr15:57211431-57211442 chr15:57211309-57211323 chr15:57210743-57210752
23	POLR2A	chr15:57209892-57212391	K562	blood:	n/a	n/a
24	TAF1	chr15:57210098-57211134	H1-neurons	neurons:	n/a	n/a
25	HEY1	chr15:57210101-57212414	K562	blood:	n/a	chr15:57210700-57210715 chr15:57211944-57211959
26	RCOR1	chr15:57209712-57211415	GM12878	blood:	n/a	n/a
27	MAX	chr15:57209863-57211107	H1-hESC	embryonic stem cell:	n/a	chr15:57210744-57210754
28	YY1	chr15:57209726-57211968	K562	blood:	n/a	chr15:57209903-57209915 chr15:57211431-57211442 chr15:57211905-57211919 chr15:57211309-57211323 chr15:57211877-57211886 chr15:57210743-57210752
29	BHLHE40	chr15:57209970-57211075	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:57210109-57211850	GM10847	blood:	n/a	n/a
31	MAX	chr15:57209946-57211021	H1-hESC	embryonic stem cell:	n/a	chr15:57210744-57210754
32	E2F4	chr15:57210088-57211195	K562	blood:	n/a	chr15:57210776-57210785 chr15:57210743-57210752 chr15:57211095-57211105 chr15:57210740-57210752
33	CTBP2	chr15:57209945-57211423	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr15:57209911-57212289	K562	blood:	n/a	n/a
35	TBP	chr15:57209819-57212677	K562	blood:	n/a	n/a
36	IRF4	chr15:57210080-57210915	GM12878	blood:	n/a	n/a
37	POLR2A	chr15:57210001-57211989	GM12878	blood:	n/a	n/a
38	BHLHE40	chr15:57209815-57211033	K562	blood:	n/a	n/a
39	POLR2A	chr15:57210014-57212234	H1-hESC	embryonic stem cell:	n/a	n/a
40	E2F6	chr15:57210070-57211023	A549	lung:	n/a	chr15:57210776-57210785 chr15:57210743-57210752 chr15:57210740-57210752
41	POLR2A	chr15:57210032-57212483	K562	blood:	n/a	n/a
42	SP1	chr15:57210019-57211187	A549	lung:	n/a	chr15:57210741-57210753 chr15:57210742-57210751 chr15:57210743-57210752 chr15:57210741-57210753 chr15:57210742-57210751 chr15:57210742-57210756 chr15:57210925-57210934
43	RELA	chr15:57209866-57212325	GM12891	blood:	n/a	n/a
44	YY1	chr15:57209746-57210146	GM12892	blood:	n/a	chr15:57209903-57209915
45	MAX	chr15:57209939-57210955	K562	blood:	n/a	chr15:57210744-57210754
46	POLR2A	chr15:57210067-57212601	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr15:57209631-57211915	K562	blood:	n/a	n/a
48	POLR2A	chr15:57210027-57212406	GM12892	blood:	n/a	n/a
49	WRNIP1	chr15:57209733-57210697	GM12878	blood:	n/a	n/a
50	PML	chr15:57210093-57211116	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:57210107-57210157	T-47D	breast:	n/a
2	chr15:57210107-57210157	AoSMC	blood vessel:	n/a
3	chr15:57210107-57210157	GM12878	blood:	n/a
4	chr15:57210107-57210157	SK-N-MC	brain:	n/a
5	chr15:57210107-57210157	HCF	heart:	n/a
6	chr15:57210107-57210157	ECC-1	luminal epithelium:	n/a
7	chr15:57210107-57210157	Hepatocyte	liver:	n/a
8	chr15:57210107-57210157	RPTEC	kidney:	n/a
9	chr15:57210107-57210157	HIPEpiC	eye:	n/a
10	chr15:57210107-57210157	HCPEpiC	choroid plexus:	n/a
11	chr15:57210107-57210157	HRCEpiC	kidney:	n/a
12	chr15:57210107-57210157	SAEC	small airway:	n/a
13	chr15:57210107-57210157	SKMC	muscle:	n/a
14	chr15:57210107-57210157	HNPCEpiC	eye:	n/a
15	chr15:57210107-57210157	HMEC	breast:	n/a
16	chr15:57210107-57210157	AG04449	skin:	fetal
17	chr15:57210107-57210157	HUVEC	blood vessel:	n/a
18	chr15:57210107-57210157	HAEpiC	amniotic membrane:	n/a
19	chr15:57210107-57210157	NHBE	bronchial:	n/a
20	chr15:57210107-57210157	CMK	blood:	n/a
21	chr15:57210107-57210157	HPAEpiC	pulmonary alveolar:	n/a
22	chr15:57210107-57210157	NH-A	brain:	n/a
23	chr15:57210107-57210157	SK-N-SH	brain:	n/a
24	chr15:57210107-57210157	GM12892	blood:	n/a
25	chr15:57210107-57210157	U87	brain:	n/a
26	chr15:57210107-57210157	GM06990	blood:	n/a
27	chr15:57210107-57210157	HEK293	kidney:	embryo
28	chr15:57210107-57210157	NT2-D1	testis:	n/a
29	chr15:57210107-57210157	HCT-116	colon:	n/a
30	chr15:57210107-57210157	GM12891	blood:	n/a
31	chr15:57210107-57210157	BJ	skin:	n/a
32	chr15:57210107-57210157	PrEC	prostate:	n/a
33	chr15:57210107-57210157	HL-60	blood:	n/a
34	chr15:57210107-57210157	H1-hESC	embryonic stem cell:	embryo
35	chr15:57210107-57210157	MCF-7	breast:	n/a
36	chr15:57210107-57210157	IMR90	lung:	fetal
37	chr15:57210107-57210157	AG10803	skin:	n/a
38	chr15:57210107-57210157	ovcar-3	ovarian:	n/a
39	chr15:57210107-57210157	K562	blood:	n/a
40	chr15:57210107-57210157	HCM	heart:	n/a
41	chr15:57210107-57210157	HEEpiC	esophagus:	n/a
42	chr15:57210107-57210157	LNCaP	prostate:	n/a
43	chr15:57210107-57210157	Caco-2	colon:	n/a
44	chr15:57210107-57210157	HRE	kidney:	n/a
45	chr15:57210107-57210157	HRPEpiC	eye:	n/a
46	chr15:57210107-57210157	PFSK-1	brain:	n/a
47	chr15:57210107-57210157	AG09309	skin:	n/a
48	chr15:57210107-57210157	ProgFib	skin:	n/a
49	chr15:57210107-57210157	AG04450	lung:	fetal
50	chr15:57210107-57210157	PANC-1	pancreas:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57023111..57027218-chr15:57209095..57213054,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MNS1-3	chr15:57209738-57210697	ENSG00000248500
2	lnc-MNS1-3	chr15:57209738-57210691	ENSG00000259484.1

Variant related genes	Relation type
ZNF280D	TF binding region
TCF12	TF binding region
TCF12	CpG island
ZNF280D	CpG island
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12593585	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593613	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594574	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16953313	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16977152	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16977165	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16977226	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs213150	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs35615435	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56193354	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57722526	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58121543	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58169256	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60056005	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60219100	1.00[EUR][1000 genomes]
rs60972002	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61382868	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74018413	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74018420	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74018424	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74018426	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74018429	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74018439	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs74018441	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74018460	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	esv3419108	chr15:57209560-57212908	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57209000-57210200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:57209000-57210200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
3	chr15:57209000-57210200	Enhancers	Spleen	Spleen
4	chr15:57209000-57210200	Flanking Active TSS	K562	blood
5	chr15:57209000-57210400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:57209000-57210400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:57209000-57210400	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr15:57209200-57210200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr15:57209200-57210200	Flanking Active TSS	Brain Hippocampus Middle	brain
10	chr15:57209200-57210200	Flanking Active TSS	Fetal Heart	heart
11	chr15:57209200-57210200	Enhancers	Small Intestine	intestine
12	chr15:57209200-57210200	Flanking Active TSS	Osteobl	bone
13	chr15:57209200-57210600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:57209200-57210600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr15:57209200-57212200	Active TSS	Stomach Smooth Muscle	stomach
16	chr15:57209200-57213000	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr15:57209200-57213000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:57209400-57210200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
19	chr15:57209400-57210200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
20	chr15:57209400-57210200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr15:57209400-57210200	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr15:57209400-57210200	Active TSS	Right Atrium	heart
23	chr15:57209400-57210400	Flanking Active TSS	Fetal Brain Male	brain
24	chr15:57209400-57211000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr15:57209400-57212200	Active TSS	Colon Smooth Muscle	Colon
26	chr15:57209400-57212800	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr15:57209400-57213200	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr15:57209400-57213400	Active TSS	HSMMtube	muscle
29	chr15:57209400-57217200	Active TSS	Thymus	Thymus
30	chr15:57209600-57210200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
31	chr15:57209600-57210200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
32	chr15:57209600-57210200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:57209600-57210200	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr15:57209600-57210200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr15:57209600-57210200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:57209600-57210200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:57209600-57210200	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr15:57209600-57210200	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr15:57209600-57210200	Flanking Active TSS	Left Ventricle	heart
40	chr15:57209600-57210200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr15:57209600-57210200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr15:57209600-57210200	Flanking Active TSS	NHEK	skin
43	chr15:57209600-57210400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:57209600-57210400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr15:57209600-57210400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr15:57209600-57210400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
47	chr15:57209600-57210400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr15:57209600-57210400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr15:57209600-57210400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:57209600-57210400	Flanking Active TSS	Colonic Mucosa	Colon

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