Variant report

Variant	rs10873979
Chromosome Location	chr1:78836908-78836909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10489785	0.81[CEU][hapmap];0.88[CHB][hapmap]
rs10782664	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782665	0.94[CHB][hapmap]
rs10873978	0.81[JPT][hapmap]
rs10873980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873983	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10873984	0.87[EUR][1000 genomes]
rs10873985	0.87[CHB][hapmap]
rs11162477	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11162478	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11162479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11162488	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs11162489	0.87[EUR][1000 genomes]
rs11162490	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs11162492	0.94[CHB][hapmap];0.80[JPT][hapmap]
rs1156031	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12049259	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs12080346	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12122274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12128334	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12132664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141234	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12717769	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12733301	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740373	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12742293	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12752083	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12756296	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1328447	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1328448	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1332254	0.94[CHB][hapmap]
rs1333069	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1333070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571366	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs1581749	0.94[CHB][hapmap]
rs1831168	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1929982	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs2208897	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs2224674	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2990698	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs4587523	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4650348	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs473910	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs482493	0.86[EUR][1000 genomes]
rs490938	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs494981	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs521636	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs523464	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs525351	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs537086	0.84[EUR][1000 genomes]
rs538855	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs540903	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs551514	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs555475	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs571456	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs583964	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes]
rs585795	0.88[EUR][1000 genomes]
rs587996	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs591889	0.86[EUR][1000 genomes]
rs595489	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs604097	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs626063	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs631280	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs632184	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs639594	0.85[EUR][1000 genomes]
rs646012	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs648572	0.86[EUR][1000 genomes]
rs663934	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6678699	0.94[CHB][hapmap]
rs678443	0.88[EUR][1000 genomes]
rs7535841	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7541577	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs789283	0.86[EUR][1000 genomes];0.95[ASN][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	nsv1013008	chr1:78463173-78958701	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv535012	chr1:78463173-78958701	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv482697	chr1:78786028-78935333	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78832400-78837800	Weak transcription	Pancreas	Pancrea
2	chr1:78833600-78837600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:78833800-78837600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:78833800-78837600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:78834600-78837600	Enhancers	HMEC	breast
6	chr1:78834600-78837800	Enhancers	HSMM	muscle
7	chr1:78834800-78837600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:78834800-78837800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:78835400-78837000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:78835600-78837400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:78835600-78837400	Enhancers	Osteobl	bone
12	chr1:78836000-78837200	Enhancers	NH-A	brain
13	chr1:78836200-78837200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:78836200-78837400	Enhancers	HSMMtube	muscle
15	chr1:78836400-78837000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:78836800-78837200	Flanking Active TSS	NHDF-Ad	bronchial
17	chr1:78836800-78837400	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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