Variant report

Variant	rs13404703
Chromosome Location	chr2:153376205-153376206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10168793	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10172230	0.90[JPT][hapmap]
rs10182254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10188611	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10207275	0.81[CHB][hapmap]
rs10209069	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10211164	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10931154	0.84[ASN][1000 genomes]
rs11904088	0.92[ASN][1000 genomes]
rs12612608	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12613219	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12619679	0.92[ASN][1000 genomes]
rs12619706	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622731	0.84[ASN][1000 genomes]
rs13427485	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16831261	0.82[CHB][hapmap]
rs16831307	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2346182	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2459776	0.81[CHB][hapmap]
rs2577180	0.81[CHB][hapmap]
rs2577181	0.81[CHB][hapmap]
rs2577182	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4664114	0.81[EUR][1000 genomes]
rs4664592	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4664593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7581544	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7591606	0.86[CHB][hapmap]
rs893331	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9288108	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs9967814	0.82[CHB][hapmap]

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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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:56 , 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	chr2:153362400-153379400	Weak transcription	Fetal Brain Male	brain
3	chr2:153365000-153377600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:153365400-153377200	Weak transcription	Small Intestine	intestine
5	chr2:153365600-153386000	Weak transcription	Fetal Stomach	stomach
6	chr2:153371000-153379200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr2:153373000-153380200	Weak transcription	Brain Germinal Matrix	brain
8	chr2:153373800-153376400	Enhancers	Brain Angular Gyrus	brain
9	chr2:153373800-153377600	Enhancers	Fetal Intestine Small	intestine
10	chr2:153374400-153376600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr2:153374400-153381200	Weak transcription	Gastric	stomach
12	chr2:153374600-153378400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:153374600-153385000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:153375000-153381600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:153375200-153376400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:153375200-153377400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:153375400-153376400	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr2:153375400-153377200	Weak transcription	A549	lung
19	chr2:153375400-153377200	Weak transcription	HepG2	liver
20	chr2:153375400-153382200	Weak transcription	Fetal Kidney	kidney
21	chr2:153375600-153376400	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:153375600-153377800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:153375600-153385000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:153375800-153376400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr2:153375800-153376400	Enhancers	HMEC	breast
26	chr2:153375800-153378000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:153375800-153379000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:153376000-153377400	Weak transcription	Stomach Mucosa	stomach
29	chr2:153376000-153377600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:153376000-153377800	Enhancers	Brain Hippocampus Middle	brain
31	chr2:153376000-153380800	Weak transcription	Aorta	Aorta
32	chr2:153376000-153380800	Weak transcription	Ovary	ovary
33	chr2:153376000-153381200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:153376000-153381400	Weak transcription	Lung	lung
35	chr2:153376000-153381400	Weak transcription	Psoas Muscle	Psoas
36	chr2:153376000-153381600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:153376000-153381600	Weak transcription	Fetal Lung	lung
38	chr2:153376000-153381600	Weak transcription	Right Atrium	heart
39	chr2:153376000-153381800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:153376000-153381800	Weak transcription	Pancreas	Pancrea
41	chr2:153376000-153382000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:153376000-153385200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:153376000-153388800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:153376200-153376400	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr2:153376200-153376600	Enhancers	Colon Smooth Muscle	Colon
46	chr2:153376200-153377400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:153376200-153378200	Weak transcription	NH-A	brain
48	chr2:153376200-153378400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:153376200-153378400	Enhancers	Brain Cingulate Gyrus	brain
50	chr2:153376200-153378400	Enhancers	Brain Substantia Nigra	brain

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