Variant report

Variant	rs1169299
Chromosome Location	chr12:121429194-121429195
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	chr12:121428875-121429488	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121419295..121421296-chr12:121428164..121430442,2	MCF-7	breast:
2	chr12:121427353..121429838-chr12:121441548..121443367,3	K562	blood:

Variant related genes	Relation type
HNF1A	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10849829	0.81[ASN][1000 genomes]
rs1169279	0.96[ASN][1000 genomes]
rs1169281	0.96[ASN][1000 genomes]
rs1169302	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1169303	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2254971	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2258043	0.96[ASN][1000 genomes]
rs2258287	0.95[ASN][1000 genomes]
rs2259690	0.96[ASN][1000 genomes]
rs2259693	0.96[ASN][1000 genomes]
rs2259777	0.95[ASN][1000 genomes]
rs2259883	0.88[ASN][1000 genomes]
rs2260399	0.81[ASN][1000 genomes]
rs2260445	0.82[ASN][1000 genomes]
rs2260446	0.82[ASN][1000 genomes]
rs2264778	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4278584	0.93[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	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	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
8	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1039216	chr12:121421701-121538491	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121418600-121441000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:121418800-121431800	Weak transcription	Fetal Stomach	stomach
3	chr12:121418800-121439400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:121419200-121431600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:121419600-121441000	Weak transcription	Small Intestine	intestine
6	chr12:121419800-121429800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:121422200-121432800	Weak transcription	Fetal Kidney	kidney
8	chr12:121423400-121431600	Weak transcription	Colonic Mucosa	Colon
9	chr12:121424400-121432800	Weak transcription	Stomach Mucosa	stomach
10	chr12:121425000-121432400	Weak transcription	A549	lung
11	chr12:121426200-121440200	Strong transcription	HepG2	liver
12	chr12:121426600-121434000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:121426800-121429800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:121427000-121431400	Weak transcription	Pancreas	Pancrea
15	chr12:121427600-121442600	Strong transcription	Fetal Intestine Large	intestine
16	chr12:121427800-121429800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:121427800-121431200	Weak transcription	Gastric	stomach
18	chr12:121427800-121431200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:121427800-121431200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:121427800-121441200	Strong transcription	Fetal Intestine Small	intestine
21	chr12:121428800-121435000	Strong transcription	Liver	Liver

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