Variant report

Variant	rs9788865
Chromosome Location	chr16:31009588-31009589
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	MAZ	chr16:31009510-31009692	HepG2	liver:	n/a	n/a
2	NFIC	chr16:31008859-31009780	HepG2	liver:	n/a	n/a
3	REST	chr16:31009353-31009755	SK-N-SH	brain:	n/a	n/a
4	MXI1	chr16:31009421-31010125	HepG2	liver:	n/a	n/a
5	TAF1	chr16:31009402-31009862	SK-N-SH	brain:	n/a	n/a
6	TEAD4	chr16:31009189-31010903	HepG2	liver:	n/a	n/a
7	MAX	chr16:31009559-31009918	K562	blood:	n/a	n/a
8	CEBPB	chr16:31009393-31009824	IMR90	lung:	n/a	n/a
9	POLR2A	chr16:31007570-31010938	HepG2	liver:	n/a	n/a
10	FOS	chr16:31009435-31009799	MCF10A-Er-Src	breast:	n/a	n/a
11	PBX3	chr16:31009330-31010101	SK-N-SH	brain:	n/a	chr16:31009737-31009746
12	GATA3	chr16:31007562-31009639	A549	lung:	n/a	chr16:31009108-31009118 chr16:31008136-31008145 chr16:31009315-31009326
13	TCF7L2	chr16:31009273-31009817	MCF-7	breast:	n/a	n/a
14	FOS	chr16:31009435-31009998	MCF10A-Er-Src	breast:	n/a	n/a
15	HEY1	chr16:31007231-31010930	HepG2	liver:	n/a	n/a
16	RAD21	chr16:31009351-31010037	Hela-S3	cervix:	n/a	chr16:31009360-31009367 chr16:31009984-31009998
17	MAX	chr16:31007512-31010112	A549	lung:	n/a	n/a
18	SIN3A	chr16:31009536-31009865	H1-hESC	embryonic stem cell:	n/a	n/a
19	SP1	chr16:31007487-31009961	A549	lung:	n/a	chr16:31008388-31008398 chr16:31008658-31008669 chr16:31008388-31008397 chr16:31008142-31008151 chr16:31008140-31008152 chr16:31009838-31009850 chr16:31008384-31008398 chr16:31008640-31008651 chr16:31008142-31008151 chr16:31007981-31007990 chr16:31008141-31008150
20	FOSL2	chr16:31009325-31009877	SK-N-SH	brain:	n/a	n/a
21	ZNF263	chr16:31008353-31010832	HEK293-T-REx	kidney:	n/a	n/a
22	RAD21	chr16:31009335-31010100	IMR90	lung:	n/a	chr16:31009360-31009367 chr16:31009984-31009998
23	POLR2A	chr16:31007616-31009917	Hela-S3	cervix:	n/a	n/a
24	CREB1	chr16:31007538-31009954	HepG2	liver:	n/a	n/a
25	POLR2A	chr16:31009474-31009790	HCT-116	colon:	n/a	n/a
26	POLR2A	chr16:31007733-31009919	Hela-S3	cervix:	n/a	n/a
27	HDAC2	chr16:31009540-31010814	HepG2	liver:	n/a	chr16:31010143-31010151
28	JUND	chr16:31008335-31010130	SK-N-SH	brain:	n/a	chr16:31009614-31009625
29	MYBL2	chr16:31008734-31009797	HepG2	liver:	n/a	n/a
30	FOSL2	chr16:31009384-31009792	A549	lung:	n/a	n/a
31	JUND	chr16:31009409-31009773	H1-hESC	embryonic stem cell:	n/a	chr16:31009614-31009625
32	JUND	chr16:31009275-31010150	SK-N-SH	brain:	n/a	chr16:31009614-31009625
33	POLR2A	chr16:31007590-31009677	HepG2	liver:	n/a	n/a
34	TCF7L2	chr16:31009464-31009793	PANC-1	pancreas:	n/a	n/a
35	JUND	chr16:31009466-31009783	K562	blood:	n/a	chr16:31009614-31009625
36	FOS	chr16:31009375-31009805	MCF10A-Er-Src	breast:	n/a	n/a
37	SMARCC1	chr16:31008222-31010120	Hela-S3	cervix:	n/a	n/a
38	RCOR1	chr16:31009418-31009671	K562	blood:	n/a	n/a
39	FOSL2	chr16:31009268-31010047	SK-N-SH	brain:	n/a	n/a
40	MAZ	chr16:31008159-31010622	IMR90	lung:	n/a	n/a
41	RFX5	chr16:31009499-31009948	Hela-S3	cervix:	n/a	n/a
42	TCF7L2	chr16:31009500-31009889	Hela-S3	cervix:	n/a	n/a
43	MAX	chr16:31007955-31010121	Hela-S3	cervix:	n/a	n/a
44	TAF1	chr16:31009388-31009807	Hela-S3	cervix:	n/a	n/a
45	FOS	chr16:31009449-31009804	MCF10A-Er-Src	breast:	n/a	n/a
46	MAX	chr16:31009494-31009810	HepG2	liver:	n/a	n/a
47	MAFK	chr16:31009367-31009834	IMR90	lung:	n/a	n/a
48	STAT3	chr16:31009296-31009898	MCF10A-Er-Src	breast:	n/a	chr16:31009483-31009494
49	MYC	chr16:31009419-31009804	MCF10A-Er-Src	breast:	n/a	n/a
50	CTCF	chr16:31009460-31009610	BJ	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:30959192..30961458-chr16:31007681..31010044,2	K562	blood:
2	chr16:31007019..31009950-chr16:31086954..31088883,2	MCF-7	breast:
3	chr16:31004363..31015645-chr16:31042809..31047717,18	MCF-7	breast:
4	chr16:31007064..31010034-chr16:31018671..31022251,4	MCF-7	breast:
5	chr16:31007135..31009873-chr16:31190289..31192804,2	MCF-7	breast:
6	chr16:31008264..31010102-chr16:31053957..31055799,2	MCF-7	breast:
7	chr16:31007054..31011428-chr16:31011544..31016044,11	MCF-7	breast:
8	chr16:31007115..31010903-chr16:31041705..31047571,13	MCF-7	breast:
9	chr16:31007911..31010328-chr16:31084206..31087011,2	K562	blood:
10	chr16:31005622..31010168-chr16:31042261..31047356,7	K562	blood:
11	chr16:30991043..31010547-chr16:31082350..31088728,42	MCF-7	breast:
12	chr16:31008630..31010759-chr16:31011117..31013438,2	K562	blood:
13	chr16:30960482..30963722-chr16:31009124..31011668,3	K562	blood:
14	chr16:31008766..31010883-chr16:31047833..31050675,2	MCF-7	breast:
15	chr16:31008781..31009709-chr19:17953009..17953805,2	Hela-S3	cervix:
16	chr16:31006807..31011358-chr16:31082999..31086095,12	MCF-7	breast:
17	chr16:31004521..31010198-chr16:31190050..31194376,11	K562	blood:
18	chr16:31008117..31009690-chr16:31151800..31154471,2	K562	blood:
19	chr16:31008825..31009679-chr5:148865004..148865943,2	Hela-S3	cervix:
20	chr16:31008272..31010092-chr17:57918270..57920367,2	MCF-7	breast:
21	chr16:30968978..30971725-chr16:31006942..31010708,4	K562	blood:
22	chr16:30998679..31000953-chr16:31008665..31011087,2	MCF-7	breast:
23	chr16:31008194..31010118-chr16:31137008..31138912,2	MCF-7	breast:
24	chr16:31008048..31010924-chr16:31103164..31107386,3	MCF-7	breast:
25	chr16:31006037..31010198-chr16:31189951..31194376,15	K562	blood:
26	chr16:31008927..31009697-chr9:115248462..115249064,2	Hela-S3	cervix:
27	chr16:31005622..31009984-chr16:31042414..31045630,5	K562	blood:

Variant related genes	Relation type
STX1B	TF binding region
ENSG00000105639	Chromatin interaction
ENSG00000099365	Chromatin interaction
ENSG00000167395	Chromatin interaction
ENSG00000255439	Chromatin interaction
ENSG00000261487	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000175938	Chromatin interaction
ENSG00000167394	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000167397	Chromatin interaction
ENSG00000103510	Chromatin interaction
ENSG00000260911	Chromatin interaction
ENSG00000178226	Chromatin interaction
ENSG00000103496	Chromatin interaction
ENSG00000230185	Chromatin interaction
ENSG00000099381	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs17708472	0.86[CEU][hapmap];0.95[GIH][hapmap]
rs2054214	0.95[GIH][hapmap]
rs2359674	0.85[CEU][hapmap];0.95[GIH][hapmap]
rs4405566	1.00[JPT][hapmap]
rs55731737	0.89[EUR][1000 genomes]
rs55908605	0.89[EUR][1000 genomes]
rs61185452	0.82[ASN][1000 genomes]
rs72800841	0.90[EUR][1000 genomes]
rs72800842	0.89[EUR][1000 genomes]
rs72800845	0.87[EUR][1000 genomes]
rs72800846	0.88[EUR][1000 genomes]
rs72800849	0.84[EUR][1000 genomes]
rs73528516	0.82[ASN][1000 genomes]
rs8046978	0.86[CEU][hapmap]
rs9927295	0.85[CEU][hapmap];0.95[GIH][hapmap]
rs9932822	0.82[ASN][1000 genomes]
rs9932921	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
2	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv1064134	chr16:30640293-31087327	Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	238 gene(s)	inside rSNPs	diseases
4	nsv905729	chr16:30642867-31247924	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
5	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
6	nsv833191	chr16:30864242-31048051	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	115 gene(s)	inside rSNPs	diseases
7	nsv905734	chr16:30877544-31191482	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
8	nsv905735	chr16:30890538-31247924	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	264 gene(s)	inside rSNPs	diseases
9	nsv905737	chr16:30900235-31014179	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
10	nsv457483	chr16:30903679-31191482	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
11	nsv571820	chr16:30903679-31191482	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	253 gene(s)	inside rSNPs	diseases
12	esv1797877	chr16:30948643-31188432	Flanking Active TSS Enhancers Weak transcription Strong transcription 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 miRNA target site	114 gene(s)	inside rSNPs	diseases
13	nsv833193	chr16:30960796-31133604	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
14	nsv916994	chr16:30971725-31078117	Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9788865	STX1B	cis	parietal	SCAN
rs9788865	QPRT	cis	parietal	SCAN
rs9788865	ZNF48	cis	cerebellum	SCAN
rs9788865	STX1B	cis	cerebellum	SCAN
rs9788865	SRCAP	cis	parietal	SCAN
rs9788865	ZNF668	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30997600-31013600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr16:31007600-31010000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr16:31007800-31009600	Bivalent Enhancer	Stomach Mucosa	stomach
4	chr16:31007800-31009800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr16:31008200-31009800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr16:31008200-31010200	Flanking Active TSS	HSMM	muscle
7	chr16:31008800-31009600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr16:31008800-31009600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr16:31008800-31009600	Flanking Active TSS	HMEC	breast
10	chr16:31008800-31009600	Flanking Active TSS	HSMMtube	muscle
11	chr16:31008800-31009600	Flanking Active TSS	NHDF-Ad	bronchial
12	chr16:31008800-31009600	Flanking Active TSS	NHEK	skin
13	chr16:31008800-31009800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:31008800-31010000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr16:31008800-31010000	Flanking Bivalent TSS/Enh	HepG2	liver
16	chr16:31008800-31010000	Flanking Active TSS	NHLF	lung
17	chr16:31008800-31010200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr16:31008800-31010200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr16:31008800-31010200	Flanking Active TSS	NH-A	brain
20	chr16:31008800-31010200	Flanking Active TSS	Osteobl	bone
21	chr16:31009000-31009800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr16:31009000-31009800	Bivalent Enhancer	Fetal Thymus	thymus
23	chr16:31009000-31009800	Enhancers	Ovary	ovary
24	chr16:31009000-31009800	Enhancers	Spleen	Spleen
25	chr16:31009000-31010200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr16:31009000-31010200	Flanking Active TSS	A549	lung
27	chr16:31009000-31010200	Flanking Active TSS	Hela-S3	cervix
28	chr16:31009000-31013200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr16:31009000-31013800	Enhancers	Liver	Liver
30	chr16:31009000-31020400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr16:31009200-31009600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr16:31009200-31009600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr16:31009200-31009600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr16:31009200-31009600	Enhancers	Pancreas	Pancrea
35	chr16:31009200-31009600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
36	chr16:31009200-31009800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr16:31009200-31009800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr16:31009200-31009800	Enhancers	Colonic Mucosa	Colon
39	chr16:31009200-31009800	Enhancers	Esophagus	oesophagus
40	chr16:31009200-31010000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr16:31009200-31010000	Weak transcription	Fetal Brain Female	brain
42	chr16:31009200-31010000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
43	chr16:31009200-31010000	Bivalent Enhancer	Fetal Muscle Leg	muscle
44	chr16:31009200-31010400	Weak transcription	Brain Germinal Matrix	brain
45	chr16:31009200-31010600	Weak transcription	Aorta	Aorta
46	chr16:31009200-31010800	Weak transcription	Colon Smooth Muscle	Colon
47	chr16:31009200-31011000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr16:31009200-31011200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr16:31009200-31011200	Enhancers	Fetal Intestine Large	intestine
50	chr16:31009200-31011200	Enhancers	Fetal Intestine Small	intestine

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