Variant report

Variant	rs3002142
Chromosome Location	chr1:222788062-222788063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2889934	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3002133	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3002134	0.81[ASN][1000 genomes]
rs3002136	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3002139	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3002143	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008598	0.89[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3008601	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3008602	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3008604	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3008606	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3008607	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3008608	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3008610	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3123300	0.85[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3002142	HHIPL2	cis	cerebellum	SCAN
rs3002142	HN1	trans	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222786400-222790600	Weak transcription	Psoas Muscle	Psoas
2	chr1:222787200-222790600	Weak transcription	K562	blood
3	chr1:222787400-222788800	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr1:222787400-222789600	Weak transcription	Liver	Liver
5	chr1:222787400-222789800	Weak transcription	HepG2	liver
6	chr1:222787400-222790600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:222787600-222788600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:222787600-222790000	Weak transcription	Stomach Mucosa	stomach
9	chr1:222787600-222790200	Weak transcription	Fetal Intestine Large	intestine
10	chr1:222787600-222790600	Weak transcription	Fetal Intestine Small	intestine

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Input of quick search could be:

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

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