Variant report

Variant	rs12230601
Chromosome Location	chr12:105350704-105350705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105349646..105353787-chr12:105376379..105382982,10	MCF-7	breast:
2	chr12:105343851..105348812-chr12:105350003..105354386,8	MCF-7	breast:
3	chr12:105345347..105347103-chr12:105350407..105353151,2	MCF-7	breast:
4	chr12:105290364..105293204-chr12:105349716..105351702,2	MCF-7	breast:
5	chr12:104349867..104352216-chr12:105350654..105352678,2	MCF-7	breast:
6	chr12:105344565..105347442-chr12:105349621..105353002,3	K562	blood:

Variant related genes	Relation type
ENSG00000204954	Chromatin interaction
ENSG00000136052	Chromatin interaction
ENSG00000265054	Chromatin interaction
ENSG00000151131	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10778357	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10861292	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10861297	0.80[EUR][1000 genomes]
rs2248978	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2252839	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2468398	0.81[AMR][1000 genomes]
rs4409923	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964116	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4964305	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs57987047	0.82[EUR][1000 genomes]
rs7133934	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7965314	0.87[AMR][1000 genomes]
rs7973707	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105338200-105351000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:105346800-105351400	Weak transcription	Small Intestine	intestine
3	chr12:105347400-105350800	Weak transcription	NHEK	skin
4	chr12:105347400-105351400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:105347800-105350800	Weak transcription	Hela-S3	cervix
6	chr12:105347800-105351000	Weak transcription	HUVEC	blood vessel
7	chr12:105349400-105351000	Weak transcription	Placenta	Placenta
8	chr12:105349400-105351000	Weak transcription	Pancreas	Pancrea
9	chr12:105350200-105351000	Weak transcription	Stomach Mucosa	stomach
10	chr12:105350400-105351200	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:105350400-105353400	Active TSS	Aorta	Aorta
12	chr12:105350600-105350800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr12:105350600-105350800	Enhancers	Adipose Nuclei	Adipose
14	chr12:105350600-105350800	Active TSS	Colon Smooth Muscle	Colon
15	chr12:105350600-105350800	Enhancers	Fetal Brain Male	brain
16	chr12:105350600-105350800	Active TSS	Fetal Brain Female	brain
17	chr12:105350600-105350800	Bivalent/Poised TSS	Fetal Kidney	kidney
18	chr12:105350600-105350800	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr12:105350600-105350800	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr12:105350600-105350800	Active TSS	Osteobl	bone
21	chr12:105350600-105351000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
22	chr12:105350600-105351000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:105350600-105351000	Flanking Active TSS	GM12878-XiMat	blood
24	chr12:105350600-105351000	Enhancers	HepG2	liver
25	chr12:105350600-105351200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:105350600-105351200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:105350600-105351200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:105350600-105351200	Flanking Active TSS	A549	lung
29	chr12:105350600-105351200	Enhancers	HSMMtube	muscle
30	chr12:105350600-105351400	Enhancers	Primary B cells from peripheral blood	blood
31	chr12:105350600-105351400	Active TSS	Fetal Stomach	stomach
32	chr12:105350600-105351600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:105350600-105351600	Flanking Active TSS	Liver	Liver
34	chr12:105350600-105351600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr12:105350600-105352000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr12:105350600-105352400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:105350600-105352400	Active TSS	Gastric	stomach
38	chr12:105350600-105352600	Active TSS	Duodenum Mucosa	Duodenum
39	chr12:105350600-105352600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr12:105350600-105352600	Active TSS	NHLF	lung
41	chr12:105350600-105353400	Active TSS	Ovary	ovary

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