Variant report

Variant	rs17405288
Chromosome Location	chr2:77113949-77113950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10520174	1.00[YRI][hapmap]
rs11901979	0.85[CEU][hapmap]
rs1319244	0.85[CEU][hapmap]
rs1446721	1.00[JPT][hapmap]
rs1517775	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17333213	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17333276	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17333303	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17333383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17333404	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17333578	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17333850	1.00[YRI][hapmap]
rs17333884	0.83[CHD][hapmap];0.94[GIH][hapmap]
rs17333926	1.00[JPT][hapmap]
rs17334506	1.00[YRI][hapmap]
rs17405433	0.85[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17405440	0.85[CEU][hapmap];0.86[CHB][hapmap]
rs17405711	0.83[CHD][hapmap];0.94[GIH][hapmap]
rs17405864	1.00[JPT][hapmap]
rs17405953	1.00[YRI][hapmap]
rs17405981	1.00[YRI][hapmap]
rs17406009	1.00[YRI][hapmap]
rs17406023	1.00[YRI][hapmap]
rs17406202	1.00[YRI][hapmap]
rs17406374	1.00[YRI][hapmap]
rs17406395	1.00[YRI][hapmap]
rs17406416	1.00[YRI][hapmap]
rs1929443	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1929444	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1929454	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1929455	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1929457	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1929458	0.81[GIH][hapmap]
rs2077823	1.00[YRI][hapmap]
rs4447628	1.00[YRI][hapmap]
rs4853285	1.00[YRI][hapmap]
rs56161148	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58061039	0.87[EUR][1000 genomes]
rs62170328	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62170330	0.80[EUR][1000 genomes]
rs62170331	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62170332	0.81[EUR][1000 genomes]
rs62173102	0.84[AMR][1000 genomes]
rs62173103	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62173104	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62173110	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6715191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6743766	0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs6759073	0.85[CEU][hapmap]
rs72819250	0.84[AMR][1000 genomes]
rs7425906	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs956657	1.00[YRI][hapmap]
rs985751	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006086	chr2:77031163-77128651	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv874321	chr2:77031247-77113949	Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv874322	chr2:77031247-77209750	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1007648	chr2:77034405-77128651	Enhancers Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv2752990	chr2:77038541-77217310	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv874323	chr2:77048896-77113949	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv874324	chr2:77048896-77201916	Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv874325	chr2:77053916-77113949	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv458274	chr2:77055883-77113949	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv582250	chr2:77055883-77113949	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv874326	chr2:77055883-77148261	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv582251	chr2:77055883-77154515	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv874327	chr2:77085752-77209750	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv525625	chr2:77096124-77113949	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv874328	chr2:77096124-77196122	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv874329	chr2:77096124-77209750	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
17	esv1819739	chr2:77103474-77162163	Enhancers Weak transcription Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv874330	chr2:77103719-77209750	Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17405288	HTRA2	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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