Variant report

Variant	rs12490566
Chromosome Location	chr3:112867990-112867991
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	chr3:112865633..112868819-chr3:112877200..112880555,3	MCF-7	breast:
2	chr3:112866581..112868430-chr3:112875306..112877224,2	K562	blood:

Variant related genes	Relation type
ENSG00000240057	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10934222	0.82[ASN][1000 genomes]
rs11923603	0.91[ASN][1000 genomes]
rs12631163	0.82[ASN][1000 genomes]
rs12631199	0.82[ASN][1000 genomes]
rs12634099	0.86[ASN][1000 genomes]
rs2204788	0.87[ASN][1000 genomes]
rs2204789	0.87[ASN][1000 genomes]
rs2700229	0.86[ASN][1000 genomes]
rs3732812	0.84[ASN][1000 genomes]
rs3995932	0.85[ASN][1000 genomes]
rs4528911	0.87[ASN][1000 genomes]
rs62264166	0.88[ASN][1000 genomes]
rs6770160	0.87[ASN][1000 genomes]
rs9855348	0.82[ASN][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112863400-112870600	Weak transcription	Left Ventricle	heart
2	chr3:112865200-112871400	Enhancers	Fetal Stomach	stomach
3	chr3:112865600-112870000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:112865600-112870000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:112865800-112870400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:112866000-112868200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr3:112866200-112868200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:112866400-112869800	Enhancers	Fetal Muscle Leg	muscle
9	chr3:112866600-112868000	Enhancers	Placenta Amnion	Placenta Amnion
10	chr3:112866600-112868200	Enhancers	Placenta	Placenta
11	chr3:112866600-112868200	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr3:112866800-112868000	Enhancers	Fetal Brain Female	brain
13	chr3:112866800-112868200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr3:112866800-112868200	Enhancers	Fetal Lung	lung
15	chr3:112866800-112869600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:112867000-112869000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:112867000-112869200	Weak transcription	Pancreas	Pancrea
18	chr3:112867200-112868200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr3:112867200-112868400	Enhancers	Fetal Intestine Small	intestine
20	chr3:112867400-112868200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:112867400-112868600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr3:112867400-112869400	Weak transcription	Fetal Intestine Large	intestine
23	chr3:112867600-112868000	Flanking Active TSS	Colon Smooth Muscle	Colon
24	chr3:112867600-112868000	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr3:112867600-112868800	Weak transcription	Esophagus	oesophagus
26	chr3:112867600-112869000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:112867600-112869000	Weak transcription	Adipose Nuclei	Adipose
28	chr3:112867600-112869000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr3:112867600-112869000	Weak transcription	Psoas Muscle	Psoas
30	chr3:112867600-112869000	Weak transcription	Right Atrium	heart
31	chr3:112867600-112869000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:112867600-112869000	Weak transcription	Spleen	Spleen
33	chr3:112867600-112869200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr3:112867600-112869600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:112867600-112870400	Weak transcription	Small Intestine	intestine
36	chr3:112867600-112870600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr3:112867600-112870600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:112867600-112870600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:112867600-112871800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:112867600-112872200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:112867600-112872800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:112867800-112868800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:112867800-112869000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:112867800-112869000	Weak transcription	Fetal Kidney	kidney
45	chr3:112867800-112872200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:112867800-112872200	Weak transcription	NHEK	skin
47	chr3:112867800-112872400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:112867800-112872400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:112867800-112872400	Weak transcription	HMEC	breast
50	chr3:112867800-112872600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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