Variant report

Variant	rs55956549
Chromosome Location	chr12:121413930-121413931
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121412159..121414001-chr12:121420552..121422609,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10849823	0.89[EUR][1000 genomes]
rs10849824	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2251556	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2254779	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2393777	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4371007	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55691424	0.80[EUR][1000 genomes]
rs7132164	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7135458	0.86[EUR][1000 genomes]
rs7303401	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73226268	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73226290	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73226296	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73228105	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73228108	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7961178	0.96[AMR][1000 genomes];0.99[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	chr12:121408000-121414200	Genic enhancers	Fetal Intestine Small	intestine
4	chr12:121408200-121417800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:121408400-121415400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:121409600-121415000	Weak transcription	Esophagus	oesophagus
7	chr12:121409600-121418400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:121409600-121422200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:121410000-121415400	Weak transcription	Fetal Kidney	kidney
10	chr12:121410000-121415400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:121410000-121418600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:121411200-121414000	Weak transcription	A549	lung
13	chr12:121411200-121415400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:121411200-121416000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:121411400-121415200	Weak transcription	Colonic Mucosa	Colon
16	chr12:121411400-121418200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr12:121411400-121418200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:121411600-121415600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:121412200-121414200	Weak transcription	Gastric	stomach
20	chr12:121412200-121415000	Weak transcription	Stomach Mucosa	stomach
21	chr12:121412200-121416000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:121412200-121416000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:121412400-121414000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:121412400-121414000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:121412400-121414000	Weak transcription	HepG2	liver
26	chr12:121412400-121414200	Weak transcription	Pancreas	Pancrea
27	chr12:121412400-121415000	Weak transcription	Fetal Stomach	stomach
28	chr12:121413000-121414000	Enhancers	Fetal Intestine Large	intestine
29	chr12:121413600-121414000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:121413800-121415200	Enhancers	Liver	Liver

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