Variant report

Variant	rs10489949
Chromosome Location	chr1:78805965-78805966
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11804627	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065075	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403178	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12406527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408096	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564401	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1328450	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340161	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34213203	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34475536	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34605360	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35042189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41292958	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv2763565	chr1:78774623-78809058	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1011898	chr1:78774623-78815799	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	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:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78804600-78806400	Enhancers	HMEC	breast
2	chr1:78804600-78806800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:78804600-78807000	Enhancers	Hela-S3	cervix
4	chr1:78804600-78808400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:78804800-78806000	Enhancers	NH-A	brain
6	chr1:78804800-78806600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr1:78804800-78806800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:78804800-78806800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:78804800-78807000	Enhancers	HUVEC	blood vessel
10	chr1:78805000-78806200	Enhancers	HSMMtube	muscle
11	chr1:78805000-78806400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:78805000-78806400	Enhancers	HSMM	muscle
13	chr1:78805000-78807000	Enhancers	NHEK	skin
14	chr1:78805000-78819800	Weak transcription	Pancreas	Pancrea
15	chr1:78805200-78806000	Enhancers	Placenta Amnion	Placenta Amnion
16	chr1:78805200-78806200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:78805400-78807600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr1:78805600-78806200	Enhancers	NHLF	lung
19	chr1:78805600-78806400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:78805600-78806400	Enhancers	Osteobl	bone
21	chr1:78805600-78808000	Enhancers	NHDF-Ad	bronchial
22	chr1:78805800-78806000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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