Variant report

Variant	rs11904088
Chromosome Location	chr2:153381728-153381729
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	chr2:153365869..153368986-chr2:153378102..153382040,3	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10165830	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10168692	0.82[AMR][1000 genomes]
rs10168793	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10172230	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10182254	0.92[ASN][1000 genomes]
rs10188611	0.90[ASN][1000 genomes]
rs10209069	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10211164	0.90[ASN][1000 genomes]
rs10931154	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12612608	0.92[ASN][1000 genomes]
rs12613219	0.93[ASN][1000 genomes]
rs12619679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619706	0.93[ASN][1000 genomes]
rs12622731	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13404703	0.92[ASN][1000 genomes]
rs13427485	0.93[ASN][1000 genomes]
rs16831307	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2346182	0.90[ASN][1000 genomes]
rs2577182	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4664592	0.93[ASN][1000 genomes]
rs4664593	0.93[ASN][1000 genomes]
rs7581544	0.93[ASN][1000 genomes]
rs893331	0.90[ASN][1000 genomes]
rs9288108	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153361000-153398600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:153365600-153386000	Weak transcription	Fetal Stomach	stomach
3	chr2:153374600-153385000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:153375400-153382200	Weak transcription	Fetal Kidney	kidney
5	chr2:153375600-153385000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:153376000-153381800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:153376000-153381800	Weak transcription	Pancreas	Pancrea
8	chr2:153376000-153382000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:153376000-153385200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:153376000-153388800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:153376200-153382800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr2:153376200-153384800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:153376200-153384800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:153376400-153381800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:153376400-153382000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:153376600-153390600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:153377800-153381800	Weak transcription	Small Intestine	intestine
18	chr2:153378000-153381800	Weak transcription	Stomach Mucosa	stomach
19	chr2:153378000-153385000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:153378400-153382000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:153378400-153382000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:153378400-153386200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:153378800-153383600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:153379000-153381800	Enhancers	HUVEC	blood vessel
25	chr2:153379200-153381800	Enhancers	Osteobl	bone
26	chr2:153379200-153382000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr2:153379200-153382200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:153379200-153382200	Enhancers	HMEC	breast
29	chr2:153379200-153383200	Enhancers	NHDF-Ad	bronchial
30	chr2:153379800-153381800	Enhancers	NH-A	brain
31	chr2:153380200-153381800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:153380400-153383200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:153380800-153383000	Enhancers	Aorta	Aorta
34	chr2:153380800-153383000	Enhancers	Ovary	ovary
35	chr2:153381000-153383600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:153381200-153382200	Enhancers	HepG2	liver
37	chr2:153381200-153383000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:153381200-153383000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr2:153381200-153383000	Enhancers	Gastric	stomach
40	chr2:153381200-153383200	Enhancers	Brain Anterior Caudate	brain
41	chr2:153381200-153384200	Enhancers	Brain Cingulate Gyrus	brain
42	chr2:153381200-153388200	Enhancers	Brain Hippocampus Middle	brain
43	chr2:153381200-153388200	Enhancers	Brain Substantia Nigra	brain
44	chr2:153381400-153382200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:153381400-153382400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:153381400-153382400	Enhancers	Colonic Mucosa	Colon
47	chr2:153381400-153382800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:153381400-153383000	Enhancers	Lung	lung
49	chr2:153381400-153383000	Enhancers	Psoas Muscle	Psoas
50	chr2:153381400-153383200	Enhancers	HSMM	muscle

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