Variant report

Variant	rs66627474
Chromosome Location	chr12:121410678-121410679
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	SP1	chr12:121410567-121411203	H1-hESC	embryonic stem cell:	n/a	chr12:121410897-121410911
2	TEAD4	chr12:121410587-121411086	HepG2	liver:	n/a	n/a
3	MAX	chr12:121410678-121411027	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:121410588-121411390	HepG2	liver:	n/a	n/a
5	TEAD4	chr12:121410654-121411076	H1-hESC	embryonic stem cell:	n/a	n/a
6	FOXA1	chr12:121410652-121411198	T-47D	breast:	n/a	n/a
7	SP1	chr12:121410655-121411028	H1-hESC	embryonic stem cell:	n/a	chr12:121410897-121410911
8	FOXA1	chr12:121410607-121411119	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:121410071-121411673	HepG2	liver:	n/a	n/a
10	FOXA1	chr12:121410672-121411146	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121410040..121412493-chr12:121417620..121420402,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf43-1	chr12:121410457-121412502	NONHSAT031257

Variant related genes	Relation type
ENSG00000272214	TF binding region
ENSG00000241388	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11065360	0.98[ASN][1000 genomes]
rs11065361	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815613	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12821745	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12826999	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28380723	0.98[ASN][1000 genomes]
rs55913575	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135408	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73226265	0.98[ASN][1000 genomes]
rs7961554	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669493	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	esv3357747	chr12:121405281-121427388	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121400600-121416000	Weak transcription	Small Intestine	intestine
2	chr12:121403800-121411000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:121405200-121415400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:121406600-121410800	Strong transcription	Rectal Mucosa Donor 31	rectum
5	chr12:121406600-121412400	Genic enhancers	Liver	Liver
6	chr12:121407400-121410800	Weak transcription	Fetal Stomach	stomach
7	chr12:121408000-121414200	Genic enhancers	Fetal Intestine Small	intestine
8	chr12:121408200-121417800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:121408400-121411000	Weak transcription	Colonic Mucosa	Colon
10	chr12:121408400-121415400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:121409000-121412400	Genic enhancers	Fetal Intestine Large	intestine
12	chr12:121409200-121412200	Enhancers	Stomach Mucosa	stomach
13	chr12:121409200-121412400	Genic enhancers	HepG2	liver
14	chr12:121409400-121410800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:121409400-121411200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:121409400-121411200	Enhancers	K562	blood
17	chr12:121409400-121411400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:121409600-121415000	Weak transcription	Esophagus	oesophagus
19	chr12:121409600-121418400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:121409600-121422200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:121409800-121410800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:121409800-121410800	Weak transcription	Placenta	Placenta
23	chr12:121410000-121410800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:121410000-121410800	Weak transcription	A549	lung
25	chr12:121410000-121411000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:121410000-121411000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:121410000-121415400	Weak transcription	Fetal Kidney	kidney
28	chr12:121410000-121415400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr12:121410000-121418600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:121410400-121412000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:121410600-121411200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:121410600-121411400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:121410600-121411400	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr12:121410600-121411800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:121410600-121411800	Genic enhancers	Pancreas	Pancrea
36	chr12:121410600-121412000	Genic enhancers	Gastric	stomach
37	chr12:121410600-121412200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:121410600-121412200	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr12:121410600-121412400	Strong transcription	Rectal Mucosa Donor 29	rectum

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