Variant report

Variant	rs12293275
Chromosome Location	chr11:66774238-66774239
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	GTF2F1	chr11:66773983-66774241	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:66773765-66774437	SK-N-MC	brain:	n/a	n/a
3	TAF1	chr11:66773933-66774430	H1-hESC	embryonic stem cell:	n/a	n/a
4	NFE2	chr11:66774025-66774282	GM12878	blood:	n/a	n/a
5	NFYB	chr11:66774009-66774368	GM12878	blood:	n/a	chr11:66774206-66774221
6	USF1	chr11:66773826-66774479	A549	lung:	n/a	chr11:66774148-66774159
7	TAF1	chr11:66773972-66774372	H1-hESC	embryonic stem cell:	n/a	n/a
8	USF1	chr11:66773812-66774406	H1-hESC	embryonic stem cell:	n/a	chr11:66774148-66774159
9	YY1	chr11:66773692-66774418	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr11:66773983-66774440	Hela-S3	cervix:	n/a	n/a
11	YY1	chr11:66773828-66774411	K562	blood:	n/a	n/a
12	HEY1	chr11:66773990-66774276	K562	blood:	n/a	n/a
13	SP1	chr11:66773849-66774561	A549	lung:	n/a	n/a
14	POLR2A	chr11:66773910-66774428	H1-neurons	neurons:	n/a	n/a
15	ATF3	chr11:66773993-66774359	K562	blood:	n/a	n/a
16	MAX	chr11:66774004-66774374	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr11:66773990-66774331	K562	blood:	n/a	n/a
18	YY1	chr11:66773949-66774245	GM12891	blood:	n/a	n/a
19	POLR2A	chr11:66774053-66774281	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr11:66773912-66774331	HCT-116	colon:	n/a	n/a
21	USF2	chr11:66773970-66774342	HepG2	liver:	n/a	chr11:66774148-66774159 chr11:66774193-66774204
22	POLR2A	chr11:66773968-66774415	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAX	chr11:66773999-66774370	NB4	blood:	n/a	n/a
24	USF1	chr11:66773963-66774407	A549	lung:	n/a	chr11:66774148-66774159
25	MAX	chr11:66774085-66774268	HepG2	liver:	n/a	n/a
26	YY1	chr11:66773731-66774357	H1-hESC	embryonic stem cell:	n/a	n/a
27	NFYA	chr11:66773965-66774434	K562	blood:	n/a	chr11:66774209-66774227
28	USF1	chr11:66774014-66774311	HepG2	liver:	n/a	chr11:66774148-66774159
29	ATF3	chr11:66773912-66774419	H1-hESC	embryonic stem cell:	n/a	n/a
30	YY1	chr11:66773870-66774344	GM12878	blood:	n/a	n/a
31	POLR2A	chr11:66773866-66774474	Hela-S3	cervix:	n/a	n/a
32	USF1	chr11:66773955-66774335	HepG2	liver:	n/a	chr11:66774148-66774159
33	YY1	chr11:66773787-66774356	A549	lung:	n/a	n/a
34	YY1	chr11:66773908-66774273	GM12892	blood:	n/a	n/a
35	NFYA	chr11:66773961-66774744	Hela-S3	cervix:	n/a	chr11:66774209-66774227
36	POLR2A	chr11:66774199-66774397	HCT-116	colon:	n/a	n/a
37	USF1	chr11:66773923-66774310	GM12878	blood:	n/a	chr11:66774148-66774159
38	USF2	chr11:66773944-66774449	K562	blood:	n/a	chr11:66774148-66774159 chr11:66774193-66774204
39	YY1	chr11:66773899-66774257	HepG2	liver:	n/a	n/a
40	USF1	chr11:66773751-66774515	H1-hESC	embryonic stem cell:	n/a	chr11:66774148-66774159
41	YY1	chr11:66773815-66774320	NT2-D1	testis:	n/a	n/a
42	YY1	chr11:66773937-66774316	K562	blood:	n/a	n/a
43	BHLHE40	chr11:66773942-66774316	K562	blood:	n/a	n/a
44	NFYB	chr11:66773967-66774642	K562	blood:	n/a	chr11:66774206-66774221
45	YY1	chr11:66773948-66774319	GM12891	blood:	n/a	n/a
46	USF1	chr11:66773787-66774652	A549	lung:	n/a	chr11:66774148-66774159
47	USF2	chr11:66774009-66774338	GM12878	blood:	n/a	chr11:66774148-66774159 chr11:66774193-66774204
48	MAX	chr11:66773921-66774322	K562	blood:	n/a	n/a
49	USF1	chr11:66773994-66774334	SK-N-SH_RA	brain:	n/a	chr11:66774148-66774159
50	YY1	chr11:66773899-66774376	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66761490..66778711-chr11:66821814..66832221,36	MCF-7	breast:
2	chr11:66772630..66777861-chr11:66788171..66792271,6	MCF-7	breast:

Variant related genes	Relation type
SYT12	TF binding region
ENSG00000173227	Chromatin interaction
ENSG00000173156	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10160663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10896146	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10896147	1.00[EUR][1000 genomes]
rs10896148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227645	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227647	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227654	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227655	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227659	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227662	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11227664	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12222286	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12270068	0.84[ASW][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12270183	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12273240	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12274897	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12275124	0.90[AFR][1000 genomes]
rs12275370	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12276046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12277065	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12277720	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12279585	0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12281292	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12281335	1.00[EUR][1000 genomes]
rs12281512	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12282433	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12282440	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12284422	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12284764	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12284808	1.00[ASW][hapmap];0.83[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12284860	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12285661	1.00[EUR][1000 genomes]
rs12287658	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12288309	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12288354	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12290308	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12290429	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12290836	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12290886	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12290950	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12292728	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12788732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56173916	1.00[EUR][1000 genomes]
rs56973649	1.00[EUR][1000 genomes]
rs57604888	1.00[EUR][1000 genomes]
rs57748654	1.00[EUR][1000 genomes]
rs57946225	1.00[EUR][1000 genomes]
rs60751057	1.00[EUR][1000 genomes]
rs7109580	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7123934	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7128943	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73493529	1.00[EUR][1000 genomes]
rs73493531	1.00[EUR][1000 genomes]
rs73501797	1.00[EUR][1000 genomes]
rs73501800	1.00[EUR][1000 genomes]
rs7924894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7925264	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7941982	1.00[ASW][hapmap];1.00[EUR][1000 genomes]
rs7942885	1.00[EUR][1000 genomes]
rs7948985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
4	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
5	esv1817552	chr11:66751014-66839985	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66772600-66776400	Weak transcription	Liver	Liver
2	chr11:66773200-66774800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr11:66773600-66774400	Flanking Active TSS	Osteobl	bone
4	chr11:66773800-66774400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr11:66773800-66774400	Enhancers	Brain Substantia Nigra	brain
6	chr11:66773800-66774600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr11:66773800-66774600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:66773800-66774600	Enhancers	Spleen	Spleen
9	chr11:66773800-66774600	Flanking Active TSS	Hela-S3	cervix
10	chr11:66773800-66775000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:66773800-66775200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr11:66774000-66774400	Enhancers	Brain Angular Gyrus	brain
13	chr11:66774000-66774400	Enhancers	Dnd41	blood
14	chr11:66774000-66774600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr11:66774000-66774600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr11:66774000-66774600	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr11:66774000-66774600	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr11:66774000-66774600	Enhancers	Brain Cingulate Gyrus	brain
19	chr11:66774000-66774600	Enhancers	Brain Hippocampus Middle	brain
20	chr11:66774000-66774600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:66774000-66774600	Active TSS	Lung	lung
22	chr11:66774000-66774800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:66774200-66774400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:66774200-66774400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:66774200-66774400	Enhancers	HepG2	liver
26	chr11:66774200-66774600	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr11:66774200-66774600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr11:66774200-66774600	Enhancers	Adipose Nuclei	Adipose
29	chr11:66774200-66774600	Enhancers	A549	lung
30	chr11:66774200-66774600	Enhancers	K562	blood
31	chr11:66774200-66774800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr11:66774200-66774800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr11:66774200-66774800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:66774200-66774800	Enhancers	Brain Anterior Caudate	brain
35	chr11:66774200-66774800	Enhancers	Placenta	Placenta

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