Variant report

Variant	rs214101
Chromosome Location	chr11:17289354-17289355
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	ELF1	chr11:17289140-17289389	A549	lung:	n/a	n/a
2	RPC155	chr11:17288992-17289418	Hela-S3	cervix:	n/a	n/a
3	FOSL1	chr11:17288834-17289655	HCT-116	colon:	n/a	n/a
4	RAD21	chr11:17289301-17289492	A549	lung:	n/a	n/a
5	ZNF384	chr11:17289237-17289546	K562	blood:	n/a	n/a
6	CHD2	chr11:17289203-17289443	Hela-S3	cervix:	n/a	n/a
7	BRCA1	chr11:17289129-17289491	Hela-S3	cervix:	n/a	n/a
8	JUND	chr11:17289147-17289432	K562	blood:	n/a	chr11:17289271-17289282
9	CTCF	chr11:17289320-17289470	SAEC	small airway:	n/a	n/a
10	RAD21	chr11:17288899-17289649	HCT-116	colon:	n/a	n/a
11	CTCF	chr11:17289280-17289430	Hela-S3	cervix:	n/a	n/a
12	USF1	chr11:17289078-17289462	A549	lung:	n/a	n/a
13	JUND	chr11:17288883-17289544	HCT-116	colon:	n/a	chr11:17289271-17289282
14	FOS	chr11:17289095-17289463	MCF10A-Er-Src	breast:	n/a	chr11:17289271-17289282
15	EP300	chr11:17289020-17289500	A549	lung:	n/a	n/a
16	ELF1	chr11:17288834-17289590	HCT-116	colon:	n/a	n/a
17	RAD21	chr11:17289171-17289557	Hela-S3	cervix:	n/a	n/a
18	FOSL2	chr11:17289067-17289420	MCF-7	breast:	n/a	n/a
19	ELF1	chr11:17289092-17289395	K562	blood:	n/a	n/a
20	CTCF	chr11:17289260-17289410	HCPEpiC	choroid plexus:	n/a	n/a
21	USF2	chr11:17289166-17289371	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr11:17289340-17289490	RPTEC	kidney:	n/a	n/a
23	E2F4	chr11:17289203-17289391	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr11:17289124-17289459	MCF10A-Er-Src	breast:	n/a	chr11:17289271-17289282
25	RCOR1	chr11:17289037-17289466	Hela-S3	cervix:	n/a	n/a
26	CEBPB	chr11:17289101-17289512	Hela-S3	cervix:	n/a	n/a
27	RFX5	chr11:17289129-17289505	Hela-S3	cervix:	n/a	n/a
28	MYC	chr11:17289121-17289439	MCF10A-Er-Src	breast:	n/a	n/a
29	RCOR1	chr11:17289213-17289393	K562	blood:	n/a	n/a
30	SIN3AK20	chr11:17288847-17289542	HCT-116	colon:	n/a	n/a
31	PRDM1	chr11:17289170-17289438	Hela-S3	cervix:	n/a	n/a
32	TEAD4	chr11:17289022-17289517	ECC-1	luminal epithelium:	n/a	n/a
33	CTCF	chr11:17289332-17289444	HUVEC	blood vessel:	n/a	n/a
34	CTCF	chr11:17289300-17289450	NHEK	skin:	n/a	n/a
35	POLR2A	chr11:17289052-17289491	HCT-116	colon:	n/a	n/a
36	JUND	chr11:17289099-17289522	Hela-S3	cervix:	n/a	chr11:17289271-17289282
37	TEAD4	chr11:17289044-17289468	K562	blood:	n/a	n/a
38	STAT3	chr11:17289119-17289465	MCF10A-Er-Src	breast:	n/a	n/a
39	CTCF	chr11:17289302-17289503	NHEK	skin:	n/a	n/a
40	JUND	chr11:17288838-17289501	HCT-116	colon:	n/a	chr11:17289271-17289282
41	JUN	chr11:17289099-17289456	HUVEC	blood vessel:	n/a	n/a
42	STAT3	chr11:17289048-17289501	MCF10A-Er-Src	breast:	n/a	n/a
43	GTF2F1	chr11:17289143-17289446	Hela-S3	cervix:	n/a	n/a
44	MAZ	chr11:17289155-17289364	Hela-S3	cervix:	n/a	n/a
45	TCF12	chr11:17289035-17289538	A549	lung:	n/a	n/a
46	TCF7L2	chr11:17289105-17289434	Hela-S3	cervix:	n/a	n/a
47	TEAD4	chr11:17288927-17289592	HCT-116	colon:	n/a	n/a
48	CTCF	chr11:17289260-17289410	HCT-116	colon:	n/a	n/a
49	CTCF	chr11:17289260-17289410	BJ	skin:	n/a	n/a
50	FOS	chr11:17289085-17289479	HUVEC	blood vessel:	n/a	chr11:17289271-17289282

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17286631..17289597-chr11:17295588..17297647,2	MCF-7	breast:
2	chr11:17287872..17290107-chr11:17373411..17375142,2	K562	blood:

Variant related genes	Relation type
NUCB2	TF binding region
ENSG00000188211	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs105290	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10766381	0.82[ASN][1000 genomes]
rs10766382	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832733	0.87[CHD][hapmap]
rs10832745	0.80[ASN][1000 genomes]
rs10832746	0.80[ASN][1000 genomes]
rs10832747	0.80[ASN][1000 genomes]
rs10832750	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10832752	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024158	0.91[CHD][hapmap]
rs11024204	0.92[CHB][hapmap];0.91[CHD][hapmap];0.80[ASN][1000 genomes]
rs11024207	0.82[ASN][1000 genomes]
rs11024208	0.82[ASN][1000 genomes]
rs11024220	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024221	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024223	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024229	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024231	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12276859	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1488933	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs190046	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1979603	0.86[ASN][1000 genomes]
rs214067	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs214069	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs214071	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs214075	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214076	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214079	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214082	0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap]
rs214083	0.92[CHB][hapmap];0.85[JPT][hapmap];0.81[YRI][hapmap];0.80[ASN][1000 genomes]
rs214084	0.80[ASN][1000 genomes]
rs214085	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs214087	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs214088	0.80[ASN][1000 genomes]
rs214092	0.91[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs214093	0.92[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs214094	0.81[ASN][1000 genomes]
rs214095	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs214097	0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs214099	0.81[ASN][1000 genomes]
rs214102	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs214900	0.91[CHD][hapmap]
rs214901	0.91[CHD][hapmap]
rs214904	0.83[EUR][1000 genomes]
rs214907	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs214910	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs214914	0.90[CHB][hapmap]
rs214923	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs214925	0.92[CHB][hapmap];0.91[CHD][hapmap]
rs214933	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs214936	0.91[CHD][hapmap]
rs214940	0.91[CHD][hapmap]
rs4508187	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs603618	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs618331	0.92[CHB][hapmap];0.80[ASN][1000 genomes]
rs677540	0.91[CHD][hapmap]
rs7108315	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7108316	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7123301	0.91[CHD][hapmap]
rs7128822	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7342262	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs7925692	0.92[CHB][hapmap];0.96[CHD][hapmap];0.84[ASN][1000 genomes]
rs7937176	0.84[ASN][1000 genomes]
rs7940253	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7949699	0.91[CHB][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467711	chr11:17027555-17320797	Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv553568	chr11:17027555-17320797	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv469762	chr11:17170690-17320691	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv482905	chr11:17170690-17320691	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs214101	OR7E14P	cis	Esophagus Mucosa	GTEx
rs214101	OR7E14P	cis	Nerve Tibial	GTEx
rs214101	NUCB2	cis	Lymphoblastoid	GTEx
rs214101	NUCB2	cis	cerebellum	SCAN
rs214101	NUCB2	Cis_1M	lymphoblastoid	RTeQTL
rs214101	NUCB2	cis	multi-tissue	Pritchard
rs214101	NUCB2	cis	lymphoblastoid	seeQTL
rs214101	TMEM86A	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17285800-17289800	Weak transcription	K562	blood
2	chr11:17286000-17289600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:17286000-17289600	Weak transcription	NHEK	skin
4	chr11:17286000-17294400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:17286000-17294400	Weak transcription	Hela-S3	cervix
6	chr11:17286000-17297200	Weak transcription	A549	lung
7	chr11:17286000-17297400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:17289000-17289400	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr11:17289000-17289400	Enhancers	Thymus	Thymus
10	chr11:17289200-17289400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr11:17289200-17289400	Enhancers	Dnd41	blood
12	chr11:17289200-17290400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:17289200-17290800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr11:17289200-17290800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr11:17289200-17291000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:17289200-17294400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:17289200-17295400	Weak transcription	Placenta	Placenta

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