Variant report

Variant	rs11646911
Chromosome Location	chr16:31483622-31483623
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	chr16:31483466-31483745	U87	brain:	n/a	n/a
2	POLR2A	chr16:31483450-31483860	ECC-1	luminal epithelium:	n/a	n/a
3	ZNF263	chr16:31483516-31484338	HEK293-T-REx	kidney:	n/a	chr16:31483720-31483741
4	CTCF	chr16:31483500-31483650	AG04449	skin:	n/a	n/a
5	POLR2A	chr16:31482818-31484664	SK-N-SH	brain:	n/a	n/a
6	MAX	chr16:31483454-31484469	ECC-1	luminal epithelium:	n/a	chr16:31483468-31483478
7	POLR2A	chr16:31483089-31483847	Gliobla	brain:	n/a	n/a
8	SIN3A	chr16:31483616-31484361	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr16:31483523-31484508	HCT-116	colon:	n/a	n/a
10	YY1	chr16:31483427-31483740	SK-N-SH_RA	brain:	n/a	chr16:31483440-31483449 chr16:31483447-31483456
11	POLR2A	chr16:31482984-31484345	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr16:31482368-31484665	HUVEC	blood vessel:	n/a	n/a
13	MAX	chr16:31483412-31484598	ECC-1	luminal epithelium:	n/a	chr16:31483448-31483458 chr16:31483468-31483478
14	SRF	chr16:31483150-31483657	ECC-1	luminal epithelium:	n/a	chr16:31483448-31483458 chr16:31483396-31483413 chr16:31483398-31483411 chr16:31483399-31483413 chr16:31483397-31483412 chr16:31483310-31483320 chr16:31483395-31483413
15	POLR2A	chr16:31483459-31483666	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr16:31483193-31483651	GM12878	blood:	n/a	chr16:31483448-31483458 chr16:31483468-31483478
17	TAF1	chr16:31483448-31484362	A549	lung:	n/a	n/a
18	POLR2A	chr16:31483108-31483925	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr16:31482818-31484752	U87	brain:	n/a	n/a
20	MAZ	chr16:31483171-31484344	Hela-S3	cervix:	n/a	chr16:31483448-31483458 chr16:31483468-31483478
21	YY1	chr16:31483509-31483942	HepG2	liver:	n/a	n/a
22	POLR2A	chr16:31483385-31484586	PFSK-1	brain:	n/a	n/a
23	MAX	chr16:31483282-31484471	A549	lung:	n/a	chr16:31483448-31483458 chr16:31483468-31483478
24	TAF1	chr16:31483450-31484526	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr16:31483009-31483818	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr16:31483576-31483671	H1-hESC	embryonic stem cell:	n/a	n/a
27	RFX5	chr16:31483592-31483846	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr16:31482535-31484727	SK-N-SH	brain:	n/a	chr16:31484226-31484235 chr16:31484229-31484247 chr16:31484230-31484246 chr16:31484222-31484235
29	POLR2A	chr16:31483390-31483639	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr16:31483445-31483811	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr16:31482491-31484623	IMR90	lung:	n/a	n/a
32	RCOR1	chr16:31482222-31484670	IMR90	lung:	n/a	n/a
33	SMARCB1	chr16:31483062-31484438	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr16:31483514-31483835	Hela-S3	cervix:	n/a	n/a
35	CTBP2	chr16:31483595-31484400	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr16:31482491-31484872	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr16:31482930-31484511	HUVEC	blood vessel:	n/a	n/a
38	TCF12	chr16:31483444-31484518	ECC-1	luminal epithelium:	n/a	n/a
39	YY1	chr16:31483010-31483888	SK-N-SH	brain:	n/a	chr16:31483440-31483449 chr16:31483284-31483295 chr16:31483447-31483456
40	CHD2	chr16:31483604-31483695	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr16:31482304-31484722	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr16:31483466-31483796	U87	brain:	n/a	n/a
43	POLR2A	chr16:31483122-31483762	A549	lung:	n/a	n/a
44	POLR2A	chr16:31483452-31483792	A549	lung:	n/a	n/a
45	POLR2A	chr16:31483069-31484005	A549	lung:	n/a	n/a
46	MAZ	chr16:31482463-31484780	IMR90	lung:	n/a	chr16:31483448-31483458 chr16:31483468-31483478
47	POLR2A	chr16:31482818-31484658	U87	brain:	n/a	n/a
48	CTCF	chr16:31483620-31483770	HEEpiC	esophagus:	n/a	n/a
49	TAF1	chr16:31483165-31484433	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr16:31483029-31483728	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:242011416..242011984-chr16:31483269..31483770,2	Hela-S3	cervix:
2	chr16:31482147..31485412-chr16:31724579..31726445,3	MCF-7	breast:
3	chr16:31463491..31466396-chr16:31481913..31484379,2	K562	blood:
4	chr16:31482449..31485901-chr16:31517810..31523430,5	MCF-7	breast:
5	chr16:31483184..31487045-chr16:31517740..31519918,3	K562	blood:
6	chr16:31483361..31485287-chr16:31723435..31725020,2	MCF-7	breast:
7	chr16:31481376..31484276-chr16:31519285..31521056,3	K562	blood:
8	chr16:31466606..31474995-chr16:31481116..31490982,25	MCF-7	breast:
9	chr16:31481496..31484305-chr16:31498079..31499870,2	MCF-7	breast:
10	chr16:31482515..31485868-chr16:31497342..31499348,3	MCF-7	breast:
11	chr16:31475154..31478732-chr16:31483245..31485698,3	MCF-7	breast:
12	chr16:31465649..31475592-chr16:31481764..31491028,24	MCF-7	breast:

Variant related genes	Relation type
TGFB1I1	TF binding region
ENSG00000260267	Chromatin interaction
ENSG00000140688	Chromatin interaction
ENSG00000174371	Chromatin interaction
ENSG00000260625	Chromatin interaction
ENSG00000140691	Chromatin interaction
ENSG00000197302	Chromatin interaction
ENSG00000260740	Chromatin interaction
ENSG00000261474	Chromatin interaction
ENSG00000140675	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11150624	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1135265	0.82[ASW][hapmap];0.88[CEU][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11643752	0.82[ASW][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs11646054	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12920273	0.81[ASN][1000 genomes]
rs12923122	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12930621	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3116150	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs35884660	0.82[ASN][1000 genomes]
rs4243237	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4313820	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4482295	0.82[ASW][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap]
rs4597343	0.82[ASN][1000 genomes]
rs4889549	0.82[JPT][hapmap]
rs4889661	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4889664	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4889666	0.82[ASN][1000 genomes]
rs7201796	0.82[ASN][1000 genomes]
rs7206531	0.82[ASN][1000 genomes]
rs8048218	0.82[ASW][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs8050563	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8050712	0.82[ASN][1000 genomes]
rs8060914	0.80[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	esv3392534	chr16:31303038-31573066	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	104 gene(s)	inside rSNPs	diseases
2	nsv833194	chr16:31358179-31528545	Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
4	nsv905748	chr16:31427678-31559220	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
5	nsv905749	chr16:31427678-31565597	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	96 gene(s)	inside rSNPs	diseases
6	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
7	nsv905751	chr16:31431360-31489033	Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	nsv905752	chr16:31436932-31565597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	95 gene(s)	inside rSNPs	diseases
9	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
10	nsv905754	chr16:31451699-31565597	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11646911	ZNF646	cis	cerebellum	SCAN
rs11646911	NCRNA00095	cis	lymphoblastoid	seeQTL
rs11646911	TGFB1I1	cis	cerebellum	SCAN
rs11646911	FBXL19	cis	cerebellum	SCAN
rs11646911	FUS	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31478800-31484000	Weak transcription	K562	blood
2	chr16:31482400-31484400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:31482600-31484200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr16:31482600-31484200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr16:31482800-31483800	Active TSS	Brain Hippocampus Middle	brain
6	chr16:31482800-31484200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:31482800-31484200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr16:31482800-31484200	Active TSS	Aorta	Aorta
9	chr16:31482800-31484200	Active TSS	Psoas Muscle	Psoas
10	chr16:31482800-31484400	Active TSS	Fetal Kidney	kidney
11	chr16:31482800-31484600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr16:31483000-31484000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr16:31483000-31484000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr16:31483000-31484000	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr16:31483000-31484000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr16:31483000-31484000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr16:31483000-31484000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr16:31483000-31484000	Bivalent/Poised TSS	Thymus	Thymus
19	chr16:31483000-31484200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
20	chr16:31483000-31484200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr16:31483000-31484200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr16:31483000-31484200	Active TSS	Esophagus	oesophagus
23	chr16:31483000-31484200	Active TSS	Fetal Heart	heart
24	chr16:31483000-31484200	Active TSS	Gastric	stomach
25	chr16:31483000-31484200	Active TSS	Left Ventricle	heart
26	chr16:31483000-31484200	Active TSS	Placenta Amnion	Placenta Amnion
27	chr16:31483000-31484400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr16:31483000-31484400	Enhancers	Fetal Brain Male	brain
29	chr16:31483000-31484400	Active TSS	Right Atrium	heart
30	chr16:31483000-31484400	Active TSS	Small Intestine	intestine
31	chr16:31483000-31484400	Active TSS	HMEC	breast
32	chr16:31483000-31484400	Active TSS	NHDF-Ad	bronchial
33	chr16:31483000-31484400	Active TSS	NHLF	lung
34	chr16:31483000-31484600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr16:31483000-31484600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr16:31483000-31484600	Active TSS	HSMM	muscle
37	chr16:31483200-31483800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr16:31483200-31483800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr16:31483200-31483800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr16:31483200-31483800	Active TSS	Fetal Intestine Large	intestine
41	chr16:31483200-31483800	Active TSS	Fetal Intestine Small	intestine
42	chr16:31483200-31483800	Active TSS	Fetal Muscle Leg	muscle
43	chr16:31483200-31483800	Active TSS	Osteobl	bone
44	chr16:31483200-31484000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
45	chr16:31483200-31484000	Active TSS	Muscle Satellite Cultured Cells	--
46	chr16:31483200-31484000	Active TSS	A549	lung
47	chr16:31483200-31484000	Active TSS	Hela-S3	cervix
48	chr16:31483200-31484000	Active TSS	HepG2	liver
49	chr16:31483200-31484000	Active TSS	HUVEC	blood vessel
50	chr16:31483200-31484000	Active TSS	NHEK	skin

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