Variant report

Variant	rs894301
Chromosome Location	chr15:78297525-78297526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:74)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:74 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:78297440-78297590	HFF-Myc	foreskin:	n/a	n/a
2	MXI1	chr15:78297109-78297985	IMR90	lung:	n/a	n/a
3	PBX3	chr15:78297041-78297947	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr15:78297420-78297570	SAEC	small airway:	n/a	n/a
5	CTCF	chr15:78297300-78297590	HCM	heart:	n/a	n/a
6	CTCF	chr15:78297380-78297530	HUVEC	blood vessel:	n/a	n/a
7	FOS	chr15:78297220-78297659	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr15:78297392-78297588	MCF10A-Er-Src	breast:	n/a	n/a
9	RAD21	chr15:78297199-78297737	SK-N-SH_RA	brain:	n/a	n/a
10	RAD21	chr15:78297150-78297731	IMR90	lung:	n/a	n/a
11	CTCF	chr15:78297440-78297590	AoAF	blood vessel:	n/a	n/a
12	FOS	chr15:78297219-78297747	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr15:78297232-78297605	MCF10A-Er-Src	breast:	n/a	n/a
14	CTCF	chr15:78297380-78297530	HMEC	breast:	n/a	n/a
15	CTCF	chr15:78297420-78297570	AG04449	skin:	n/a	n/a
16	CTCF	chr15:78297440-78297590	BE2_C	brain:	n/a	n/a
17	CTCF	chr15:78297400-78297550	HBMEC	blood vessel:	n/a	n/a
18	CTCF	chr15:78297424-78297538	ProgFib	skin:	n/a	n/a
19	ZNF263	chr15:78297281-78297748	HEK293-T-REx	kidney:	n/a	n/a
20	CTCF	chr15:78297478-78297584	Spleen_OC	spleen:	n/a	n/a
21	CTCF	chr15:78297380-78297530	SK-N-SH_RA	brain:	n/a	n/a
22	CTCF	chr15:78297359-78297533	Lung_OC	lung:	n/a	n/a
23	CTCF	chr15:78297400-78297550	AG09319	gingival:	n/a	n/a
24	CTCF	chr15:78297440-78297590	AG10803	skin:	n/a	n/a
25	MAZ	chr15:78297005-78297935	IMR90	lung:	n/a	chr15:78297408-78297418 chr15:78297361-78297370
26	CTCF	chr15:78297420-78297570	HUVEC	blood vessel:	n/a	n/a
27	CTCF	chr15:78297400-78297550	HPAF	blood vessel:	n/a	n/a
28	CTCF	chr15:78297400-78297550	AoAF	blood vessel:	n/a	n/a
29	CTCF	chr15:78297380-78297530	HCM	heart:	n/a	n/a
30	STAT3	chr15:78297384-78297699	MCF10A-Er-Src	breast:	n/a	chr15:78297541-78297552
31	CTCF	chr15:78297401-78297544	SK-N-SH_RA	brain:	n/a	n/a
32	PBX3	chr15:78297088-78297870	SK-N-SH	brain:	n/a	n/a
33	CTCF	chr15:78297420-78297570	HFF	foreskin:	n/a	n/a
34	SIN3AK20	chr15:78297215-78297689	PFSK-1	brain:	n/a	n/a
35	CTCF	chr15:78297298-78297653	IMR90	lung:	n/a	n/a
36	CTCF	chr15:78297460-78297610	NHLF	lung:	n/a	n/a
37	CTCF	chr15:78297380-78297530	HFF-Myc	foreskin:	n/a	n/a
38	CTCF	chr15:78297380-78297530	HCPEpiC	choroid plexus:	n/a	n/a
39	CEBPB	chr15:78297175-78298030	IMR90	lung:	n/a	n/a
40	SIN3AK20	chr15:78297271-78297548	PFSK-1	brain:	n/a	n/a
41	CTCF	chr15:78297400-78297550	HVMF	connective:	n/a	n/a
42	CTCF	chr15:78297468-78297541	Kidney_OC	kidney:	n/a	n/a
43	CTCF	chr15:78297400-78297550	HCPEpiC	choroid plexus:	n/a	n/a
44	CTCF	chr15:78297400-78297550	AG09309	skin:	n/a	n/a
45	CTCF	chr15:78297420-78297570	AG09309	skin:	n/a	n/a
46	CEBPB	chr15:78297204-78297982	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr15:78297400-78297550	AG04449	skin:	n/a	n/a
48	SIN3AK20	chr15:78297254-78297789	SK-N-SH	brain:	n/a	n/a
49	CTCF	chr15:78297400-78297550	HPF	lung:	n/a	n/a
50	CTCF	chr15:78297400-78297550	BJ	skin:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78297126..78298972-chr15:78298978..78301840,2	MCF-7	breast:

No data

Variant related genes	Relation type
TBC1D2B	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10444863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10519181	1.00[ASW][hapmap];0.84[CEU][hapmap]
rs12593545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1442293	0.84[CEU][hapmap]
rs16969422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17477813	1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[ASN][1000 genomes]
rs1837913	0.84[CEU][hapmap]
rs2044099	0.84[CEU][hapmap]
rs35472584	0.88[CEU][hapmap]
rs3784326	1.00[ASW][hapmap]
rs4395040	1.00[ASW][hapmap]
rs4886989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886992	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56357772	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs872926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv1833316	chr15:78081307-78328108	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs894301	PSMA4	cis	cerebellum	SCAN
rs894301	IDH3A	cis	cerebellum	SCAN
rs894301	MORF4L1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78283400-78305000	Weak transcription	K562	blood
2	chr15:78283600-78300800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:78283800-78301000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:78284600-78310200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr15:78285400-78304400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:78285800-78299200	Strong transcription	Fetal Intestine Large	intestine
7	chr15:78285800-78309600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:78286000-78310400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr15:78287000-78316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:78288400-78311000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr15:78288600-78303000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:78288600-78304400	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:78288600-78309600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr15:78288600-78309600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:78288600-78309600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:78288600-78309600	Strong transcription	Thymus	Thymus
17	chr15:78288800-78304800	Weak transcription	Fetal Kidney	kidney
18	chr15:78288800-78309600	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr15:78288800-78310400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr15:78289000-78309800	Strong transcription	Primary T cells from cord blood	blood
21	chr15:78289400-78299200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:78289400-78309800	Strong transcription	Dnd41	blood
23	chr15:78291800-78302400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:78293000-78298800	Strong transcription	Primary B cells from cord blood	blood
25	chr15:78293200-78309400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:78293600-78310000	Strong transcription	Primary hematopoietic stem cells	blood
27	chr15:78293800-78309600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:78294000-78297800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr15:78294000-78299200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr15:78294200-78299200	Weak transcription	Small Intestine	intestine
31	chr15:78294400-78300800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr15:78295200-78301200	Genic enhancers	Fetal Thymus	thymus
33	chr15:78295400-78297800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:78295400-78298200	Weak transcription	NHEK	skin
35	chr15:78295600-78298600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:78295600-78300200	Weak transcription	Aorta	Aorta
37	chr15:78295600-78301000	Genic enhancers	Rectal Mucosa Donor 31	rectum
38	chr15:78295600-78301400	Genic enhancers	Gastric	stomach
39	chr15:78295600-78305600	Enhancers	Pancreas	Pancrea
40	chr15:78295800-78297800	Enhancers	Brain Germinal Matrix	brain
41	chr15:78295800-78298000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:78295800-78298000	Genic enhancers	GM12878-XiMat	blood
43	chr15:78295800-78299400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr15:78295800-78300000	Weak transcription	HMEC	breast
45	chr15:78295800-78301200	Genic enhancers	Rectal Smooth Muscle	rectum
46	chr15:78295800-78303200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:78295800-78303200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr15:78295800-78304400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:78295800-78304600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:78296000-78297800	Enhancers	Right Ventricle	heart

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