Variant report

Variant	rs17399648
Chromosome Location	chr2:153385865-153385866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10497107	0.82[JPT][hapmap]
rs10497108	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10497111	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs11678890	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002771	1.00[JPT][hapmap]
rs16823807	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs16831392	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs16831399	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs16831410	0.82[JPT][hapmap]
rs16831413	0.82[JPT][hapmap]
rs17327752	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2678299	1.00[JPT][hapmap]
rs35552611	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664591	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434081	1.00[JPT][hapmap]
rs6434082	1.00[JPT][hapmap]
rs6706231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573833	1.00[JPT][hapmap]
rs7575177	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599894	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs9753431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:50 , 50 per page) page: 1

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	chr2:153376000-153388800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:153376600-153390600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:153378400-153386200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:153381200-153388200	Enhancers	Brain Hippocampus Middle	brain
7	chr2:153381200-153388200	Enhancers	Brain Substantia Nigra	brain
8	chr2:153382400-153386800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:153382400-153393400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:153382400-153398800	Weak transcription	Fetal Intestine Small	intestine
11	chr2:153382600-153386800	Weak transcription	Stomach Mucosa	stomach
12	chr2:153382800-153386200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:153382800-153387000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:153383000-153386000	Weak transcription	Adipose Nuclei	Adipose
15	chr2:153383000-153386400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:153383000-153387400	Weak transcription	Fetal Kidney	kidney
17	chr2:153383000-153387800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:153383000-153388000	Weak transcription	Psoas Muscle	Psoas
19	chr2:153383000-153390800	Weak transcription	Ovary	ovary
20	chr2:153383000-153391000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:153383000-153391200	Weak transcription	Aorta	Aorta
22	chr2:153383000-153392000	Weak transcription	Lung	lung
23	chr2:153383000-153403000	Weak transcription	Right Atrium	heart
24	chr2:153383200-153388400	Weak transcription	NHDF-Ad	bronchial
25	chr2:153383200-153393200	Weak transcription	NHEK	skin
26	chr2:153383600-153391400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:153384000-153398200	Weak transcription	HMEC	breast
28	chr2:153384200-153387200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr2:153384600-153388000	Enhancers	Brain Cingulate Gyrus	brain
30	chr2:153384800-153386400	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr2:153384800-153386400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:153384800-153386600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr2:153384800-153386600	Enhancers	Brain Angular Gyrus	brain
34	chr2:153384800-153386800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr2:153384800-153387000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr2:153384800-153388000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:153385000-153386000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:153385000-153386200	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr2:153385000-153386200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:153385000-153386600	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr2:153385000-153387000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:153385000-153387000	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr2:153385000-153387000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr2:153385000-153387800	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr2:153385200-153387600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:153385400-153386400	Enhancers	Small Intestine	intestine
47	chr2:153385400-153388400	Enhancers	Brain Anterior Caudate	brain
48	chr2:153385600-153387000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:153385600-153390600	Weak transcription	HepG2	liver
50	chr2:153385800-153386200	Weak transcription	H9 Cell Line	embryonic stem cell

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