Variant report

Variant	rs10863665
Chromosome Location	chr1:222032682-222032683
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11118877	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12047353	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12140184	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12144971	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4240931	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4846731	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6604679	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6604680	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6604682	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7540791	0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10863665	HHIPL2	cis	cerebellum	SCAN
rs10863665	AIDA	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222019800-222047600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:222031400-222033000	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:222031400-222033200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:222031600-222032800	Enhancers	HMEC	breast
5	chr1:222031800-222032800	Enhancers	NHEK	skin
6	chr1:222031800-222033000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:222031800-222033200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:222031800-222033400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:222032000-222032800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:222032000-222032800	Enhancers	NHDF-Ad	bronchial
11	chr1:222032000-222032800	Enhancers	Osteobl	bone
12	chr1:222032000-222033000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:222032400-222036600	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:222032600-222033800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:222032600-222038600	Weak transcription	HSMM	muscle

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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