Variant report

Variant	rs12578158
Chromosome Location	chr12:12490308-12490309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12487375..12490317-chr12:12509840..12512376,2	MCF-7	breast:
2	chr12:12489787..12492519-chr12:12503031..12504558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165714	Chromatin interaction
ENSG00000111261	Chromatin interaction
ENSG00000205791	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11054817	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11054824	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11054827	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11054832	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11054839	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs12580693	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2417091	0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35626354	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4328285	0.92[ASN][1000 genomes]
rs4763818	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56895024	0.97[AMR][1000 genomes]
rs7295350	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv898807	chr12:12448948-12502001	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv898808	chr12:12463407-12549503	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv898809	chr12:12488067-12509314	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12473200-12501600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:12473600-12493200	Weak transcription	Fetal Brain Female	brain
3	chr12:12473600-12502000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:12473800-12491800	Weak transcription	Left Ventricle	heart
5	chr12:12473800-12502400	Weak transcription	NHLF	lung
6	chr12:12477200-12491800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:12480400-12490800	Weak transcription	Right Atrium	heart
8	chr12:12480400-12502400	Weak transcription	Right Ventricle	heart
9	chr12:12481200-12491000	Weak transcription	Hela-S3	cervix
10	chr12:12481200-12495400	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:12481200-12502200	Weak transcription	Fetal Heart	heart
12	chr12:12481800-12502400	Weak transcription	Psoas Muscle	Psoas
13	chr12:12482400-12502200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:12483600-12502800	Weak transcription	Spleen	Spleen
15	chr12:12484800-12491800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr12:12485400-12500200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:12485400-12502400	Weak transcription	Esophagus	oesophagus
18	chr12:12485400-12502800	Weak transcription	Gastric	stomach
19	chr12:12485400-12502800	Weak transcription	Small Intestine	intestine
20	chr12:12486800-12491400	Weak transcription	Primary T cells from cord blood	blood
21	chr12:12486800-12491800	Weak transcription	Brain Angular Gyrus	brain
22	chr12:12487000-12491000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:12487200-12491400	Weak transcription	Aorta	Aorta
24	chr12:12487200-12491800	Weak transcription	Ovary	ovary
25	chr12:12487200-12502600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:12487400-12491000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr12:12487400-12502200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:12487400-12502200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:12487600-12502200	Weak transcription	Colonic Mucosa	Colon
30	chr12:12487800-12491000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr12:12487800-12491200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr12:12487800-12491200	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr12:12487800-12492800	Weak transcription	Brain Anterior Caudate	brain
34	chr12:12487800-12492800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr12:12488000-12490800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:12488000-12490800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:12488000-12491000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr12:12488000-12491000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:12488000-12491600	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:12488000-12491600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:12488000-12493000	Weak transcription	Brain Substantia Nigra	brain
42	chr12:12488000-12493200	Weak transcription	Adipose Nuclei	Adipose
43	chr12:12488000-12493800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:12488000-12494000	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:12488000-12495000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:12488000-12495800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:12488000-12495800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:12488000-12502000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:12488200-12490400	Weak transcription	Primary B cells from cord blood	blood
50	chr12:12488200-12490600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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