Variant report

Variant	rs13333093
Chromosome Location	chr16:30407269-30407270
allele	A/C
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	TAF1	chr16:30405653-30407431	H1-hESC	embryonic stem cell:	n/a	n/a
2	EBF1	chr16:30407104-30407494	GM12878	blood:	n/a	chr16:30407299-30407310
3	CTBP2	chr16:30406532-30407299	H1-hESC	embryonic stem cell:	n/a	n/a
4	MXI1	chr16:30406527-30407290	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr16:30406462-30407418	ECC-1	luminal epithelium:	n/a	chr16:30407025-30407037 chr16:30407025-30407035 chr16:30407023-30407036 chr16:30407020-30407039
6	MYC	chr16:30406480-30407287	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:30406351-30407456	HCT-116	colon:	n/a	n/a
8	GABPA	chr16:30406419-30407351	HepG2	liver:	n/a	n/a
9	CTCF	chr16:30406309-30407498	A549	lung:	n/a	chr16:30407022-30407035 chr16:30407019-30407037 chr16:30406917-30406930
10	MXI1	chr16:30406388-30407374	HepG2	liver:	n/a	n/a
11	RUNX3	chr16:30406914-30407373	GM12878	blood:	n/a	n/a
12	MXI1	chr16:30406250-30407665	IMR90	lung:	n/a	n/a
13	MAZ	chr16:30406506-30407452	GM12878	blood:	n/a	n/a
14	GATA2	chr16:30407216-30407896	HUVEC	blood vessel:	n/a	chr16:30407705-30407715 chr16:30407708-30407717 chr16:30407708-30407715 chr16:30407787-30407794 chr16:30407783-30407799 chr16:30407308-30407316 chr16:30407780-30407801 chr16:30407787-30407794 chr16:30407701-30407722 chr16:30407707-30407717 chr16:30407646-30407653 chr16:30407787-30407794 chr16:30407704-30407720
15	CTCF	chr16:30407260-30407410	GM12872	blood:	n/a	n/a
16	MYC	chr16:30406469-30407411	K562	blood:	n/a	n/a
17	UBTF	chr16:30405890-30407417	K562	blood:	n/a	n/a
18	SIN3AK20	chr16:30407097-30407330	A549	lung:	n/a	n/a
19	MAX	chr16:30406350-30407503	ECC-1	luminal epithelium:	n/a	n/a
20	TBL1XR1	chr16:30407174-30407842	K562	blood:	n/a	n/a
21	CHD2	chr16:30407187-30407437	GM12878	blood:	n/a	n/a
22	MAX	chr16:30406967-30407507	SK-N-SH	brain:	n/a	n/a
23	MAX	chr16:30406964-30407286	K562	blood:	n/a	n/a
24	RAD21	chr16:30406325-30407428	HepG2	liver:	n/a	chr16:30407025-30407037 chr16:30407025-30407035 chr16:30407023-30407036 chr16:30407020-30407039
25	GATA3	chr16:30406981-30407948	MCF-7	breast:	n/a	chr16:30407705-30407715 chr16:30407708-30407717 chr16:30407708-30407715 chr16:30407787-30407794 chr16:30407783-30407799 chr16:30407308-30407316 chr16:30407645-30407653 chr16:30407780-30407801 chr16:30407787-30407794 chr16:30407701-30407722 chr16:30407707-30407717 chr16:30407646-30407653 chr16:30407787-30407794 chr16:30407704-30407720
26	POLR2A	chr16:30407156-30407462	Hela-S3	cervix:	n/a	n/a
27	MAX	chr16:30406157-30407332	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr16:30405528-30407907	H1-neurons	neurons:	n/a	n/a
29	HDAC2	chr16:30406925-30407292	K562	blood:	n/a	n/a
30	SIN3AK20	chr16:30406334-30407530	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr16:30406123-30407447	ProgFib	skin:	n/a	n/a
32	RCOR1	chr16:30406419-30407855	K562	blood:	n/a	n/a
33	RFX5	chr16:30407061-30407303	HepG2	liver:	n/a	n/a
34	CTCF	chr16:30406919-30407270	A549	lung:	n/a	chr16:30407022-30407035 chr16:30407019-30407037
35	POLR2A	chr16:30406434-30407321	GM15510	blood:	n/a	n/a
36	JUND	chr16:30406365-30407390	A549	lung:	n/a	n/a
37	POLR2A	chr16:30406933-30407335	K562	blood:	n/a	n/a
38	MXI1	chr16:30406981-30407518	Hela-S3	cervix:	n/a	n/a
39	MAZ	chr16:30406397-30407447	K562	blood:	n/a	n/a
40	TAF1	chr16:30406311-30407441	HepG2	liver:	n/a	n/a
41	TAF1	chr16:30406293-30407507	ECC-1	luminal epithelium:	n/a	n/a
42	HDAC2	chr16:30406345-30407401	HepG2	liver:	n/a	n/a
43	GATA2	chr16:30407063-30407953	SH-SY5Y	brain:	n/a	chr16:30407705-30407715 chr16:30407708-30407717 chr16:30407708-30407715 chr16:30407787-30407794 chr16:30407783-30407799 chr16:30407308-30407316 chr16:30407780-30407801 chr16:30407787-30407794 chr16:30407701-30407722 chr16:30407707-30407717 chr16:30407646-30407653 chr16:30407787-30407794 chr16:30407704-30407720
44	ZBTB7A	chr16:30407195-30407434	K562	blood:	n/a	n/a
45	PAX5	chr16:30406446-30407317	GM12892	blood:	n/a	chr16:30407051-30407068
46	ZEB1	chr16:30406511-30407374	GM12878	blood:	n/a	chr16:30407188-30407201
47	TCF12	chr16:30406253-30407454	ECC-1	luminal epithelium:	n/a	chr16:30406926-30406936
48	MAX	chr16:30406347-30407271	HepG2	liver:	n/a	n/a
49	MAX	chr16:30406262-30407630	A549	lung:	n/a	n/a
50	MYBL2	chr16:30406285-30407771	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30374634..30377122-chr16:30405649..30407903,2	K562	blood:
2	chr16:30405548..30408419-chr16:30620470..30622922,2	MCF-7	breast:
3	chr16:30405344..30408453-chr16:30439632..30442076,3	MCF-7	breast:
4	chr16:30386182..30395144-chr16:30402818..30414477,44	MCF-7	breast:
5	chr16:30385968..30392864-chr16:30403786..30414800,30	MCF-7	breast:
6	chr16:30387676..30396507-chr16:30404234..30411930,28	K562	blood:
7	chr16:30406965..30407478-chr16:30662235..30662825,2	K562	blood:
8	chr16:30405223..30408007-chr16:30567849..30569998,3	MCF-7	breast:
9	chr16:30405261..30407569-chr16:30455597..30457105,2	MCF-7	breast:
10	chr16:30364578..30368660-chr16:30404559..30407754,8	MCF-7	breast:
11	chr16:30345604..30348863-chr16:30403977..30407853,5	MCF-7	breast:
12	chr16:30406017..30408531-chr16:30454989..30457376,2	MCF-7	breast:
13	chr16:30368801..30385970-chr16:30403825..30413311,30	MCF-7	breast:
14	chr16:30405726..30407812-chr16:30662378..30664163,2	K562	blood:
15	chr16:30380806..30383330-chr16:30405774..30407377,2	K562	blood:
16	chr16:30366042..30367681-chr16:30406512..30408947,2	MCF-7	breast:
17	chr16:30379558..30384763-chr16:30404117..30407449,5	MCF-7	breast:
18	chr16:30384243..30394929-chr16:30405602..30409736,14	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D10B-1	chr16:30406989-30407312	NONHSAT141744

Variant related genes	Relation type
SEPT1	TF binding region
ENSG00000180035	Chromatin interaction
ENSG00000179918	Chromatin interaction
ENSG00000183604	Chromatin interaction
ENSG00000156853	Chromatin interaction
ENSG00000169221	Chromatin interaction
ENSG00000169217	Chromatin interaction
ENSG00000179958	Chromatin interaction
ENSG00000156858	Chromatin interaction
ENSG00000180209	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000260219	Chromatin interaction
ENSG00000270466	Chromatin interaction
ENSG00000260869	Chromatin interaction
ENSG00000169951	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11150586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11646130	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs11862806	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs11863150	0.87[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12446288	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12447833	0.92[ASN][1000 genomes]
rs12921440	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12929884	0.83[LWK][hapmap];0.93[YRI][hapmap]
rs35480350	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs35598865	1.00[JPT][hapmap]
rs3574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4340343	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4465620	0.87[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4787642	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4787643	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs4788409	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs4788413	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4788414	0.82[EUR][1000 genomes]
rs62055459	0.90[ASN][1000 genomes]
rs6565182	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs6565183	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7203359	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8046445	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8049108	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs8050812	1.00[JPT][hapmap]
rs8051096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8060853	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9888967	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv962197	chr16:30390489-30425618	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	nsv1782	chr16:30391812-30410266	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	esv3325798	chr16:30405476-30408024	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13333093	MAPK3	cis	parietal	SCAN
rs13333093	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs13333093	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL
rs13333093	TBX6	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30405000-30407400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:30405000-30407600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:30405400-30407600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr16:30405400-30407800	Active TSS	Fetal Kidney	kidney
5	chr16:30405600-30407400	Active TSS	Hela-S3	cervix
6	chr16:30405600-30407600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr16:30405600-30407800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr16:30405600-30407800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr16:30405800-30407400	Active TSS	H1 Cell Line	embryonic stem cell
10	chr16:30405800-30407400	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr16:30405800-30407400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr16:30405800-30407400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr16:30405800-30407400	Active TSS	Right Ventricle	heart
14	chr16:30405800-30407400	Bivalent/Poised TSS	HepG2	liver
15	chr16:30405800-30407400	Active TSS	NHLF	lung
16	chr16:30405800-30407600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr16:30405800-30407600	Active TSS	Aorta	Aorta
18	chr16:30405800-30407800	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr16:30405800-30407800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr16:30405800-30407800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr16:30405800-30407800	Active TSS	NHDF-Ad	bronchial
22	chr16:30405800-30408000	Active TSS	H9 Cell Line	embryonic stem cell
23	chr16:30405800-30408000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr16:30405800-30408000	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr16:30405800-30408000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:30405800-30408000	Active TSS	Right Atrium	heart
27	chr16:30405800-30408200	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr16:30406000-30407400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr16:30406000-30407400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr16:30406000-30407400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr16:30406000-30407400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr16:30406000-30407400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr16:30406000-30407400	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr16:30406000-30407400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr16:30406000-30407400	Active TSS	Brain Germinal Matrix	brain
36	chr16:30406000-30407400	Active TSS	Brain Substantia Nigra	brain
37	chr16:30406000-30407400	Active TSS	Colon Smooth Muscle	Colon
38	chr16:30406000-30407400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr16:30406000-30407400	Active TSS	Fetal Intestine Large	intestine
40	chr16:30406000-30407400	Active TSS	Fetal Lung	lung
41	chr16:30406000-30407400	Active TSS	Fetal Stomach	stomach
42	chr16:30406000-30407400	Active TSS	Placenta Amnion	Placenta Amnion
43	chr16:30406000-30407400	Active TSS	Psoas Muscle	Psoas
44	chr16:30406000-30407400	Active TSS	GM12878-XiMat	blood
45	chr16:30406000-30407400	Active TSS	HSMMtube	muscle
46	chr16:30406000-30407600	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr16:30406000-30407600	Active TSS	Ovary	ovary
48	chr16:30406000-30407800	Active TSS	Fetal Brain Female	brain
49	chr16:30406000-30407800	Active TSS	Left Ventricle	heart
50	chr16:30406000-30408000	Active TSS	A549	lung

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