Variant report

Variant	rs2464190
Chromosome Location	chr12:121415390-121415391
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	chr12:121415325-121419806	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:121414963-121419793	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:121415336-121415767	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
HNF1A	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10774579	0.87[ASN][1000 genomes]
rs1169286	0.83[ASN][1000 genomes]
rs1169289	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1696359	0.82[ASN][1000 genomes]
rs1732391	0.85[ASN][1000 genomes]
rs1920792	0.93[ASN][1000 genomes]
rs2251468	0.86[ASN][1000 genomes]
rs2255531	0.91[ASN][1000 genomes]
rs2393775	0.81[EUR][1000 genomes]
rs2393776	0.81[EUR][1000 genomes]
rs2393791	0.80[EUR][1000 genomes]
rs2393792	0.83[ASN][1000 genomes]
rs2650000	0.87[ASN][1000 genomes]
rs2701175	0.85[ASN][1000 genomes]
rs6489786	0.91[ASN][1000 genomes]
rs7135337	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7139079	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7305618	0.92[ASN][1000 genomes]
rs7953249	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7954039	0.91[ASN][1000 genomes]
rs7954331	0.91[ASN][1000 genomes]
rs7970695	0.80[EUR][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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121400600-121416000	Weak transcription	Small Intestine	intestine
2	chr12:121405200-121415400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:121408200-121417800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:121408400-121415400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:121409600-121418400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:121409600-121422200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:121410000-121415400	Weak transcription	Fetal Kidney	kidney
8	chr12:121410000-121415400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:121410000-121418600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:121411200-121415400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:121411200-121416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:121411400-121418200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:121411400-121418200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:121411600-121415600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:121412200-121416000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:121412200-121416000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:121414200-121417600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
18	chr12:121414400-121415400	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr12:121414400-121415600	Enhancers	Pancreas	Pancrea
20	chr12:121414600-121415400	Weak transcription	A549	lung
21	chr12:121414600-121415600	Active TSS	Fetal Intestine Large	intestine
22	chr12:121414600-121418800	Active TSS	Gastric	stomach
23	chr12:121414600-121419000	Weak transcription	Fetal Lung	lung
24	chr12:121415000-121415600	Active TSS	Fetal Stomach	stomach
25	chr12:121415000-121415600	Enhancers	Stomach Mucosa	stomach
26	chr12:121415000-121415800	Flanking Active TSS	HepG2	liver
27	chr12:121415200-121415600	Active TSS	Colonic Mucosa	Colon
28	chr12:121415200-121415600	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr12:121415200-121415800	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr12:121415200-121416200	Flanking Active TSS	Liver	Liver

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