Variant report

Variant	rs12090909
Chromosome Location	chr1:94138784-94138785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94137739..94141828-chr1:94278104..94280351,3	MCF-7	breast:
2	chr1:93912586..93914525-chr1:94137709..94139922,2	MCF-7	breast:
3	chr1:94130370..94133890-chr1:94136641..94140326,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137942	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11164952	1.00[AMR][1000 genomes]
rs11164960	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082128	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088912	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12096357	1.00[AMR][1000 genomes]
rs72961375	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2755338	chr1:94059579-94176079	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94127400-94143800	Genic enhancers	HMEC	breast
2	chr1:94127400-94144000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:94129200-94144800	Weak transcription	GM12878-XiMat	blood
4	chr1:94130800-94141000	Genic enhancers	HSMM	muscle
5	chr1:94131200-94144000	Genic enhancers	Placenta	Placenta
6	chr1:94131400-94140600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:94131600-94143800	Genic enhancers	NHEK	skin
8	chr1:94131800-94140400	Genic enhancers	NHDF-Ad	bronchial
9	chr1:94132400-94139600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:94132800-94141000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:94132800-94141800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:94132800-94141800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:94132800-94142400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:94132800-94142600	Enhancers	Adipose Nuclei	Adipose
15	chr1:94132800-94144600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:94133000-94141600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:94133000-94142000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:94133400-94141800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:94134400-94140800	Genic enhancers	Osteobl	bone
20	chr1:94134800-94139200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:94135000-94139200	Enhancers	Left Ventricle	heart
22	chr1:94135000-94140600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:94135200-94139600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:94135200-94141200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:94135200-94141400	Enhancers	Fetal Intestine Large	intestine
26	chr1:94135200-94142400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:94135400-94142800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:94136000-94144200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:94136000-94144800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:94136200-94139400	Genic enhancers	NH-A	brain
31	chr1:94136200-94139800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:94136200-94140000	Enhancers	Fetal Intestine Small	intestine
33	chr1:94136200-94140400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:94136200-94141000	Weak transcription	Brain Angular Gyrus	brain
35	chr1:94136200-94141800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:94136400-94143000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:94136800-94139000	Enhancers	K562	blood
38	chr1:94136800-94139400	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:94137000-94138800	Enhancers	Right Ventricle	heart
40	chr1:94137000-94139000	Enhancers	Ovary	ovary
41	chr1:94137000-94139000	Enhancers	Right Atrium	heart
42	chr1:94137000-94139200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:94137000-94139400	Enhancers	Colon Smooth Muscle	Colon
44	chr1:94137000-94139400	Enhancers	Fetal Heart	heart
45	chr1:94137000-94142600	Enhancers	Fetal Lung	lung
46	chr1:94137200-94138800	Enhancers	Spleen	Spleen
47	chr1:94137200-94139200	Enhancers	Liver	Liver
48	chr1:94137200-94139400	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr1:94137400-94141000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:94137400-94141200	Enhancers	Duodenum Smooth Muscle	Duodenum

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