Variant report

Variant	rs12058171
Chromosome Location	chr1:222913107-222913108
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10495200	0.89[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11118971	1.00[ASN][1000 genomes]
rs11487815	0.86[ASW][hapmap];0.88[MKK][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes]
rs17163384	0.84[MKK][hapmap]
rs17163431	0.86[ASW][hapmap];0.87[LWK][hapmap];0.91[MKK][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17163437	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163441	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17466896	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474333	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17532610	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35684750	0.91[MEX][hapmap]
rs35762933	0.91[MEX][hapmap]
rs3748631	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41424447	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124898	0.82[EUR][1000 genomes]
rs9286760	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441846	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441936	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12058171	HHIPL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222906200-222914000	Weak transcription	K562	blood
2	chr1:222907600-222913400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:222908200-222913200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr1:222908800-222915600	Weak transcription	GM12878-XiMat	blood
5	chr1:222910000-222916800	Weak transcription	Fetal Intestine Large	intestine
6	chr1:222910200-222918200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:222910400-222913200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:222910800-222914400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr1:222910800-222915200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr1:222911200-222913400	Active TSS	Stomach Mucosa	stomach
11	chr1:222911200-222913600	Weak transcription	Liver	Liver
12	chr1:222911200-222916800	Weak transcription	Fetal Intestine Small	intestine
13	chr1:222911400-222913400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:222911600-222913200	Weak transcription	Primary T cells from cord blood	blood
15	chr1:222911600-222913600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:222912600-222914000	Active TSS	Fetal Stomach	stomach
17	chr1:222913000-222913200	Enhancers	Primary B cells from cord blood	blood
18	chr1:222913000-222915600	Enhancers	Primary B cells from peripheral blood	blood

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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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