Variant report

Variant	rs1490997
Chromosome Location	chr2:180055857-180055858
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10497535	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs11891072	0.92[AMR][1000 genomes]
rs11892241	0.82[AFR][1000 genomes]
rs11897308	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900884	0.82[AFR][1000 genomes]
rs11901408	0.88[YRI][hapmap];0.92[AMR][1000 genomes]
rs11901421	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11903685	0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11904657	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16866635	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs16866636	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs16866647	1.00[MEX][hapmap]
rs16866665	0.81[AFR][1000 genomes]
rs16866667	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2044477	0.90[AFR][1000 genomes]
rs3731739	1.00[ASW][hapmap];0.88[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs3816345	1.00[ASW][hapmap];0.84[LWK][hapmap];0.92[MKK][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs6433758	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6433759	0.81[AFR][1000 genomes]
rs6433762	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6433763	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6433765	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs6707001	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6710100	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6723850	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6725309	0.82[YRI][hapmap]
rs6728401	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6745433	0.81[AMR][1000 genomes]
rs6746115	1.00[MEX][hapmap]
rs6752298	0.80[AFR][1000 genomes]
rs7566810	0.88[ASW][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs7598995	0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7608106	0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs930620	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]

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	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	esv1807721	chr2:180024167-180076733	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179980000-180056800	Weak transcription	HSMM	muscle
2	chr2:179998000-180060600	Weak transcription	Right Ventricle	heart
3	chr2:180015000-180056000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:180015000-180060600	Weak transcription	Lung	lung
5	chr2:180015400-180058000	Weak transcription	Fetal Stomach	stomach
6	chr2:180015400-180060600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:180032200-180067600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:180037600-180058800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:180041000-180057000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:180041200-180056000	Weak transcription	Fetal Thymus	thymus
11	chr2:180041200-180058800	Weak transcription	Left Ventricle	heart
12	chr2:180041200-180058800	Weak transcription	Ovary	ovary
13	chr2:180043600-180058800	Weak transcription	Gastric	stomach
14	chr2:180046000-180057600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:180046400-180061000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:180051400-180057400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:180051800-180057800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:180052200-180056400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:180052400-180056200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:180052600-180056400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:180053200-180056000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr2:180053200-180056800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:180054400-180056000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:180054400-180056200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:180054600-180056200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:180054600-180056200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:180054800-180056200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:180054800-180056200	ZNF genes & repeats	Fetal Lung	lung
29	chr2:180055000-180056200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:180055000-180056200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:180055000-180056200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr2:180055000-180056400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr2:180055000-180057200	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:180055200-180056800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:180055200-180057200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:180055200-180058800	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:180055200-180066800	Weak transcription	Fetal Kidney	kidney
38	chr2:180055400-180056200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:180055400-180056200	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr2:180055400-180056400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:180055600-180056400	Strong transcription	Primary B cells from cord blood	blood
42	chr2:180055800-180056200	ZNF genes & repeats	Liver	Liver
43	chr2:180055800-180056400	ZNF genes & repeats	Fetal Muscle Leg	muscle
44	chr2:180055800-180057000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr2:180055800-180057200	Enhancers	HepG2	liver

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