Variant report

Variant	rs729482
Chromosome Location	chr16:31016970-31016971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr16:31016912-31017196	HEK293-T-REx	kidney:	n/a	chr16:31016995-31017016
2	ZNF384	chr16:31016571-31017009	K562	blood:	n/a	n/a
3	CEBPB	chr16:31016955-31017145	K562	blood:	n/a	n/a
4	FOS	chr16:31016913-31017112	MCF10A-Er-Src	breast:	n/a	n/a
5	RCOR1	chr16:31016486-31018377	IMR90	lung:	n/a	n/a
6	FOS	chr16:31016912-31017180	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr16:31016834-31017601	IMR90	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:31014981..31017878-chr16:31019821..31021502,2	MCF-7	breast:
2	chr16:31015311..31017608-chr16:31032189..31035035,2	MCF-7	breast:
3	chr16:31015069..31017104-chr16:31061235..31063220,2	K562	blood:
4	chr16:31007063..31009126-chr16:31016617..31018445,2	MCF-7	breast:
5	chr16:31016193..31017724-chr16:31190060..31191679,2	MCF-7	breast:
6	chr16:31015384..31017554-chr16:31043816..31046429,2	MCF-7	breast:
7	chr16:30996824..30999265-chr16:31015674..31017246,2	K562	blood:

No data

Variant related genes	Relation type
STX1B	TF binding region
ENSG00000103496	Chromatin interaction
ENSG00000089280	Chromatin interaction
ENSG00000099365	Chromatin interaction
ENSG00000268863	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1046276	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs1060506	1.00[JPT][hapmap]
rs10782001	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10782002	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap]
rs10871454	1.00[JPT][hapmap]
rs11076	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11150599	0.88[JPT][hapmap]
rs11150600	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs11150601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs11150604	1.00[JPT][hapmap]
rs11640534	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs11640961	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11649653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11862744	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs11864839	1.00[JPT][hapmap]
rs11865038	0.83[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11865499	1.00[JPT][hapmap]
rs12445568	1.00[CEU][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs12445650	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs12447930	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12597511	1.00[JPT][hapmap]
rs12920772	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12924903	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs12926295	0.88[JPT][hapmap]
rs12928852	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs12930545	1.00[CHB][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap]
rs12931046	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap]
rs13708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs14235	1.00[JPT][hapmap]
rs1458201	1.00[CHB][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap]
rs1458202	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs1549293	1.00[JPT][hapmap]
rs1870293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1978487	1.00[JPT][hapmap]
rs2032915	1.00[JPT][hapmap]
rs2054213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs2199036	0.91[EUR][1000 genomes]
rs2303222	1.00[JPT][hapmap]
rs2303223	1.00[JPT][hapmap]
rs2305880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs2305884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs2359612	1.00[JPT][hapmap]
rs28360557	0.81[EUR][1000 genomes]
rs2855475	1.00[JPT][hapmap]
rs34454770	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468353	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs35675346	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs3751855	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs3813020	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap]
rs4468641	0.83[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs4527034	1.00[JPT][hapmap]
rs4889525	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs4889599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs4889603	0.89[JPT][hapmap]
rs4889604	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap]
rs4889606	0.89[JPT][hapmap]
rs4889609	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs4889651	0.88[JPT][hapmap]
rs4889653	0.88[JPT][hapmap]
rs55979739	0.80[EUR][1000 genomes]
rs61239537	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6565217	0.83[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs6950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes]
rs7184567	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7196726	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7197717	0.83[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs7199949	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs7200879	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs7203999	1.00[CEU][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs7204459	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap]
rs7206511	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs72800847	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7294	0.83[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs732172	0.91[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs732173	0.80[EUR][1000 genomes]
rs749670	1.00[JPT][hapmap]
rs749671	1.00[JPT][hapmap]
rs749767	1.00[JPT][hapmap]
rs750952	0.83[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs8046707	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs8050588	0.83[CEU][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs8050894	1.00[JPT][hapmap]
rs8056842	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs8060857	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs8062719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs8063565	0.88[JPT][hapmap]
rs881929	1.00[JPT][hapmap]
rs889548	1.00[JPT][hapmap]
rs889555	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs897986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs9319588	0.83[CEU][hapmap]
rs9923231	1.00[JPT][hapmap]
rs9926533	0.89[JPT][hapmap]
rs9933843	0.88[JPT][hapmap]
rs9934438	1.00[JPT][hapmap]
rs9936329	1.00[JPT][hapmap]
rs9938550	0.96[CEU][hapmap];0.97[GIH][hapmap];0.83[EUR][1000 genomes]
rs9939417	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
10	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
11	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
12	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
13	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs729482	STX4	cis	lymphoblastoid	seeQTL
rs729482	MYST1	cis	lymphoblastoid	seeQTL
rs729482	STX4	Cis_1M	lymphoblastoid	RTeQTL
rs729482	MYST1	cis	parietal	SCAN
rs729482	TAOK2	cis	parietal	SCAN
rs729482	RABEP2	cis	cerebellum	SCAN
rs729482	MYST1	cis	cerebellum	SCAN
rs729482	ZNF48	cis	cerebellum	SCAN
rs729482	KAT8	cis	Skin Sun Exposed Lower leg	GTEx
rs729482	VKORC1	Cis_1M	lymphoblastoid	RTeQTL
rs729482	RP11-196G11.2	cis	lung	GTEx
rs729482	STX1B	cis	Thyroid	GTEx
rs729482	YPEL3	cis	parietal	SCAN
rs729482	VKORC1	cis	cerebellum	SCAN
rs729482	MYST1	Cis_1M	lymphoblastoid	RTeQTL
rs729482	ZNF747	cis	parietal	SCAN
rs729482	NCRNA00095	cis	cerebellum	SCAN
rs729482	ZNF785	cis	lymphoblastoid	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31009000-31020400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr16:31009200-31020400	Weak transcription	Brain Angular Gyrus	brain
3	chr16:31009200-31034400	Weak transcription	Right Atrium	heart
4	chr16:31009400-31020600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr16:31009800-31021000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr16:31010200-31020800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr16:31010600-31017600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr16:31011000-31017000	Weak transcription	Fetal Brain Female	brain
9	chr16:31011200-31018600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr16:31011200-31019800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr16:31012600-31020400	Weak transcription	Brain Germinal Matrix	brain
12	chr16:31013200-31018800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr16:31013800-31017600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr16:31013800-31021000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr16:31014000-31017000	Weak transcription	K562	blood
16	chr16:31014000-31017200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr16:31014000-31017200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr16:31014000-31017400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr16:31014200-31017200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:31014200-31019200	Weak transcription	HMEC	breast
21	chr16:31014200-31019600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr16:31014400-31018600	Weak transcription	NH-A	brain
23	chr16:31014400-31019200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr16:31014600-31019000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr16:31014800-31017200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr16:31015000-31017400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr16:31015400-31020600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr16:31015600-31017000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr16:31015800-31020600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr16:31016400-31017000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr16:31016800-31017000	Bivalent Enhancer	HepG2	liver
32	chr16:31016800-31017400	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr16:31016800-31021000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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