Variant report

Variant	rs1293989
Chromosome Location	chr1:186267100-186267101
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1293970	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1293971	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1293987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1293988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs857588	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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	esv3424090	chr1:185679718-186270877	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1293989	IVNS1ABP	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186259000-186270400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:186259600-186273600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:186259800-186268400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:186260000-186269400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:186260800-186269400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:186262400-186268800	Weak transcription	Primary T cells from cord blood	blood
7	chr1:186264600-186267200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:186265000-186267200	Enhancers	Hela-S3	cervix
9	chr1:186265200-186271200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:186265600-186279400	Weak transcription	A549	lung
11	chr1:186266600-186267400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:186266800-186267200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:186266800-186267400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:186267000-186267200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:186267000-186267400	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:186267000-186267400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:186267000-186267400	Flanking Active TSS	Liver	Liver
18	chr1:186267000-186267800	Enhancers	Fetal Thymus	thymus

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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