Variant report

Variant	rs2790689
Chromosome Location	chr1:154059815-154059816
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11264824	0.86[JPT][hapmap]
rs11265238	0.81[CEU][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs11265425	0.81[JPT][hapmap]
rs11802893	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs12025237	0.82[JPT][hapmap]
rs12026177	0.81[CEU][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs12026615	0.86[JPT][hapmap]
rs12028949	0.81[CEU][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs16835846	0.81[CEU][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap]
rs16835852	0.81[CEU][hapmap];0.83[JPT][hapmap]
rs2274993	0.82[JPT][hapmap]
rs2494669	0.94[YRI][hapmap]
rs3001361	0.94[YRI][hapmap]
rs34752019	0.86[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap]
rs3762340	0.82[JPT][hapmap]
rs3790613	0.82[JPT][hapmap]
rs3811453	0.82[JPT][hapmap]
rs3811455	0.81[CEU][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs3828077	0.82[JPT][hapmap]
rs3935419	0.81[CEU][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap]
rs4459102	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap]
rs4620534	0.81[CEU][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap]
rs6665098	0.93[YRI][hapmap]
rs6671009	0.86[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap]
rs6673752	0.82[JPT][hapmap]

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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2790689	HAX1	cis	parietal	SCAN
rs2790689	HAX1	cis	cerebellum	SCAN
rs2790689	PIP5K1A	cis	cerebellum	SCAN
rs2790689	HAX1	cis	lymphoblastoid	seeQTL
rs2790689	RAB13	cis	parietal	SCAN
rs2790689	DENND4B	cis	parietal	SCAN
rs2790689	C1orf43	cis	cerebellum	SCAN
rs2790689	SLC27A3	cis	lymphoblastoid	seeQTL
rs2790689	FAM189B	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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