Variant report

Variant	rs13329455
Chromosome Location	chr15:49912768-49912769
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	chr15:49912722-49913526	HCT-116	colon:	n/a	n/a
2	POLR2A	chr15:49911978-49916148	MCF10A-Er-Src	breast:	n/a	n/a
3	POU2F2	chr15:49912731-49913496	GM12878	blood:	n/a	n/a
4	REST	chr15:49912653-49913762	MCF-7	breast:	n/a	n/a
5	ZKSCAN1	chr15:49912447-49913429	Hela-S3	cervix:	n/a	n/a
6	ZMIZ1	chr15:49912763-49913666	K562	blood:	n/a	n/a
7	PML	chr15:49912707-49913695	MCF-7	breast:	n/a	n/a
8	TAF1	chr15:49912684-49913611	A549	lung:	n/a	n/a
9	MAZ	chr15:49912768-49913834	Hela-S3	cervix:	n/a	chr15:49913252-49913261 chr15:49913099-49913109
10	GATA1	chr15:49912693-49914184	PBDE	blood:	n/a	chr15:49914171-49914178
11	GABPA	chr15:49912747-49913461	A549	lung:	n/a	n/a
12	CEBPB	chr15:49912366-49912792	ECC-1	luminal epithelium:	n/a	chr15:49912644-49912656 chr15:49912542-49912555
13	POU2F2	chr15:49912766-49913450	GM12891	blood:	n/a	n/a
14	POLR2A	chr15:49912705-49913521	SK-N-MC	brain:	n/a	n/a
15	RFX5	chr15:49912757-49913419	H1-hESC	embryonic stem cell:	n/a	chr15:49913162-49913176 chr15:49913164-49913173
16	MAX	chr15:49912381-49913539	Hela-S3	cervix:	n/a	chr15:49913252-49913261 chr15:49913099-49913109
17	POLR2A	chr15:49912666-49913763	MCF-7	breast:	n/a	n/a
18	RXRA	chr15:49912720-49913366	HepG2	liver:	n/a	n/a
19	BCLAF1	chr15:49912740-49913567	K562	blood:	n/a	n/a
20	SIN3AK20	chr15:49912381-49914189	MCF-7	breast:	n/a	n/a
21	MAFK	chr15:49912486-49913369	K562	blood:	n/a	n/a
22	GABPA	chr15:49912342-49913659	MCF-7	breast:	n/a	n/a
23	POLR2A	chr15:49912675-49913540	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr15:49912484-49913506	GM12878	blood:	n/a	n/a
25	GATA3	chr15:49912155-49913837	MCF-7	breast:	n/a	chr15:49912499-49912510
26	ARID3A	chr15:49912442-49913424	K562	blood:	n/a	n/a
27	POLR2A	chr15:49912749-49913623	MCF-7	breast:	n/a	n/a
28	POLR2A	chr15:49912713-49913554	PANC-1	pancreas:	n/a	n/a
29	POLR2A	chr15:49912723-49913474	GM12891	blood:	n/a	n/a
30	POLR2A	chr15:49912513-49913512	K562	blood:	n/a	n/a
31	MAX	chr15:49912425-49914140	MCF-7	breast:	n/a	chr15:49913252-49913261 chr15:49913099-49913109
32	E2F4	chr15:49912754-49913465	MCF10A-Er-Src	breast:	n/a	n/a
33	CBX3	chr15:49912752-49913548	HCT-116	colon:	n/a	n/a
34	ELK4	chr15:49912329-49913427	Hela-S3	cervix:	n/a	n/a
35	RAD21	chr15:49912584-49913641	MCF-7	breast:	n/a	n/a
36	MTA3	chr15:49912597-49913603	GM12878	blood:	n/a	n/a
37	POLR2A	chr15:49912636-49914075	HL-60	blood:	n/a	n/a
38	BCLAF1	chr15:49912648-49913518	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:49912628-49913820	GM19099	blood:	n/a	n/a
40	STAT3	chr15:49912262-49913263	Hela-S3	cervix:	n/a	chr15:49913203-49913223 chr15:49912544-49912552 chr15:49912382-49912390
41	EBF1	chr15:49912671-49913529	GM12878	blood:	n/a	n/a
42	BRCA1	chr15:49912741-49913335	H1-hESC	embryonic stem cell:	n/a	n/a
43	HCFC1	chr15:49912741-49913506	K562	blood:	n/a	n/a
44	MAX	chr15:49912717-49913606	HCT-116	colon:	n/a	chr15:49913252-49913261 chr15:49913099-49913109
45	POLR2A	chr15:49912751-49913495	GM12878	blood:	n/a	n/a
46	REST	chr15:49912732-49913533	HL-60	blood:	n/a	n/a
47	POLR2A	chr15:49912500-49914069	PBDE	blood:	n/a	n/a
48	ZNF217	chr15:49912422-49914036	MCF-7	breast:	n/a	n/a
49	POLR2A	chr15:49912524-49913574	U87	brain:	n/a	n/a
50	POLR2A	chr15:49912571-49913876	GM18951	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46766106..46766752-chr15:49912745..49913620,2	NB4	blood:
2	chr15:49912192..49914242-chr15:50166228..50169006,2	MCF-7	breast:
3	chr15:49912687..49913620-chr20:25371398..25371935,2	NB4	blood:
4	chr11:62430414..62433224-chr15:49912377..49914448,2	MCF-7	breast:
5	chr15:49101837..49104427-chr15:49910988..49914617,3	K562	blood:
6	chr10:73975310..73976029-chr15:49912550..49913820,3	NB4	blood:

Variant related genes	Relation type
DTWD1	TF binding region
ENSG00000100997	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000104043	Chromatin interaction
ENSG00000103995	Chromatin interaction
ENSG00000138303	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000259700	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000166295	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10519233	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070707	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs12901416	0.84[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs12902107	0.84[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs12902794	0.84[CEU][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1354918	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395900	0.86[EUR][1000 genomes]
rs1546424	0.84[CEU][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs1546425	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs1588127	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400706	0.81[MEX][hapmap]
rs17402569	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17404262	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478618	0.81[MEX][hapmap]
rs17480434	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481696	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17483139	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814711	0.81[EUR][1000 genomes]
rs2413947	0.84[EUR][1000 genomes]
rs2413958	0.88[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs2413963	0.84[CEU][hapmap]
rs28393768	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28408092	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28409376	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28430272	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28465200	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484276	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28492008	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28516445	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28568399	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635979	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28669217	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28671247	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28798135	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28843724	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3210227	0.89[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774539	0.84[CEU][hapmap];0.86[TSI][hapmap]
rs7178101	0.81[EUR][1000 genomes]
rs8034473	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs8038373	0.82[EUR][1000 genomes]
rs8040436	0.84[CEU][hapmap]
rs8040716	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs967892	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs967893	0.84[CEU][hapmap]
rs9920033	1.00[YRI][hapmap]
rs9920574	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920705	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569392	chr15:49789413-49926300	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv431388	chr15:49835663-49997483	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs13329455	DTWD1	cis	cerebellum	SCAN
rs13329455	SECISBP2L	cis	cerebellum	SCAN
rs13329455	TRPM7	cis	cerebellum	SCAN
rs13329455	CEP152	cis	cerebellum	SCAN
rs13329455	TNFAIP8L3	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49898200-49912800	Weak transcription	Esophagus	oesophagus
2	chr15:49911200-49914200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr15:49911400-49916000	Active TSS	Stomach Smooth Muscle	stomach
4	chr15:49911600-49913800	Active TSS	Brain Angular Gyrus	brain
5	chr15:49911600-49914600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr15:49911600-49914600	Active TSS	Right Atrium	heart
7	chr15:49911600-49916600	Active TSS	GM12878-XiMat	blood
8	chr15:49911800-49912800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:49911800-49912800	Weak transcription	Left Ventricle	heart
10	chr15:49911800-49912800	Weak transcription	Pancreas	Pancrea
11	chr15:49911800-49914200	Active TSS	Psoas Muscle	Psoas
12	chr15:49911800-49914800	Active TSS	K562	blood
13	chr15:49911800-49915200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:49912000-49912800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:49912000-49913800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:49912000-49913800	Active TSS	NH-A	brain
17	chr15:49912000-49914000	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr15:49912000-49914000	Active TSS	Brain Cingulate Gyrus	brain
19	chr15:49912000-49914200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:49912000-49914200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr15:49912000-49914200	Active TSS	Right Ventricle	heart
22	chr15:49912000-49914400	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr15:49912000-49914400	Active TSS	Aorta	Aorta
24	chr15:49912000-49914400	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr15:49912000-49914600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:49912000-49915000	Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr15:49912200-49912800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr15:49912200-49912800	Flanking Active TSS	Adipose Nuclei	Adipose
29	chr15:49912200-49912800	Flanking Active TSS	Fetal Brain Female	brain
30	chr15:49912200-49912800	Flanking Active TSS	Hela-S3	cervix
31	chr15:49912200-49913800	Active TSS	Primary T cells fromperipheralblood	blood
32	chr15:49912200-49913800	Active TSS	Thymus	Thymus
33	chr15:49912200-49914000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:49912200-49914000	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr15:49912200-49914000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:49912200-49914200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:49912200-49914200	Active TSS	Colonic Mucosa	Colon
38	chr15:49912200-49914200	Active TSS	Fetal Intestine Large	intestine
39	chr15:49912200-49914200	Active TSS	Fetal Kidney	kidney
40	chr15:49912200-49914400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:49912200-49914400	Active TSS	Colon Smooth Muscle	Colon
42	chr15:49912200-49914400	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr15:49912200-49914400	Active TSS	Fetal Muscle Trunk	muscle
44	chr15:49912200-49914600	Active TSS	H1 Cell Line	embryonic stem cell
45	chr15:49912200-49914600	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr15:49912200-49914600	Active TSS	Ovary	ovary
47	chr15:49912200-49914600	Active TSS	A549	lung
48	chr15:49912200-49914600	Active TSS	HSMMtube	muscle
49	chr15:49912200-49914800	Active TSS	ES-I3 Cell Line	embryonic stem cell
50	chr15:49912200-49914800	Active TSS	HUES6 Cell Line	embryonic stem cell

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