Variant report

Variant	rs2488407
Chromosome Location	chr1:197641890-197641891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10733088	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1472498	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1499594	1.00[AMR][1000 genomes]
rs1499595	1.00[AMR][1000 genomes]
rs1580811	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1747819	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1775455	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2221133	1.00[AMR][1000 genomes]
rs2255086	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2477062	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2488399	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3933162	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4628536	1.00[AMR][1000 genomes]
rs4915247	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4915571	1.00[AMR][1000 genomes]
rs6428414	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs733876	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7518074	1.00[AMR][1000 genomes]
rs942437	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs953508	1.00[AMR][1000 genomes]
rs957939	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873074	chr1:197464448-197698103	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv873075	chr1:197464448-197714851	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv548872	chr1:197529218-197644581	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv873076	chr1:197529218-197689967	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv437263	chr1:197599030-197722240	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv873077	chr1:197615391-197698103	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197596600-197644800	Weak transcription	Ovary	ovary
2	chr1:197603200-197645000	Weak transcription	Esophagus	oesophagus
3	chr1:197603400-197643400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:197611800-197644800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:197612200-197642200	Weak transcription	Primary B cells from cord blood	blood
6	chr1:197612800-197644800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:197612800-197645000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:197628800-197645000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:197629000-197644600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:197629000-197645000	Weak transcription	Dnd41	blood
11	chr1:197629000-197645200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:197633800-197644600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:197638000-197644600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:197638600-197644600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:197640200-197644400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:197640600-197642000	Weak transcription	Fetal Lung	lung
17	chr1:197640600-197642400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:197640600-197643600	Weak transcription	NHDF-Ad	bronchial
19	chr1:197640600-197644600	Weak transcription	K562	blood
20	chr1:197640800-197642800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:197640800-197643400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:197640800-197644200	Enhancers	Liver	Liver
23	chr1:197640800-197644400	Weak transcription	Osteobl	bone
24	chr1:197640800-197644800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:197640800-197644800	Weak transcription	Fetal Intestine Small	intestine
26	chr1:197640800-197647000	Weak transcription	Small Intestine	intestine
27	chr1:197640800-197657600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:197641000-197642600	Weak transcription	Fetal Brain Male	brain
29	chr1:197641200-197643600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:197641800-197644600	Weak transcription	A549	lung
31	chr1:197641800-197645000	Weak transcription	Rectal Mucosa Donor 31	rectum

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