Variant report

Variant	rs28655875
Chromosome Location	chr3:85481015-85481016
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:85468729..85471491-chr3:85479728..85483045,3	K562	blood:

Extended variants
information (count: 147 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1025531	0.85[CHB][hapmap]
rs1030721	0.85[CHB][hapmap]
rs10511075	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs10511076	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs10511081	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs10511083	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs10511085	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs10511087	0.96[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap]
rs10865610	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs11127890	0.85[CHB][hapmap]
rs11127896	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs11919099	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs12494446	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs12633762	0.85[CHB][hapmap]
rs12637027	0.82[TSI][hapmap]
rs12638040	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap]
rs12638482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12638798	0.89[TSI][hapmap]
rs12639564	0.89[CEU][hapmap]
rs1368740	0.85[CHB][hapmap]
rs1375545	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1375551	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs1375554	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs1375555	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs1375557	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1375566	0.88[CEU][hapmap]
rs1449372	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1449373	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1449380	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1449382	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1449386	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs1449390	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1449391	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs1449405	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1449409	0.85[CHB][hapmap]
rs1463205	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs1463206	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs1463208	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1470635	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1530738	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1530739	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1530740	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs1542248	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs1549979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs1597315	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs17022915	0.84[CHB][hapmap]
rs17023019	0.91[TSI][hapmap]
rs17023032	0.89[CEU][hapmap]
rs17456763	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs17456820	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs17459563	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs17460701	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs17515586	0.87[CEU][hapmap]
rs17516256	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs17516284	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs17516346	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs17517121	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs17518584	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs17519241	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1865250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1865251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1865252	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs1868532	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1900914	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1900916	0.91[TSI][hapmap]
rs1900918	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs1947221	0.91[CEU][hapmap]
rs1991872	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs2029130	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs2029132	0.89[CEU][hapmap]
rs2029133	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs2033526	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2053108	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs2069123	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2082556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs2117151	0.82[CHB][hapmap]
rs2117153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2122233	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs2167044	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs2167045	0.83[CEU][hapmap]
rs2167047	0.95[CEU][hapmap]
rs2326309	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs2326319	0.91[TSI][hapmap]
rs2326320	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs2875907	0.91[TSI][hapmap]
rs35827242	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs4441668	0.92[CEU][hapmap];0.85[CHB][hapmap]
rs4502590	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs4856271	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs4856572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4856590	0.89[CEU][hapmap]
rs4856596	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs6549024	0.85[CHB][hapmap]
rs6549036	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs6549039	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs6549040	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs6549041	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs6549043	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs6762535	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs6762733	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs6766690	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs6779752	0.82[TSI][hapmap]
rs6780968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs6788098	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs6790090	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs6790699	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs6794866	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs6801823	0.85[CEU][hapmap];0.85[CHB][hapmap]
rs6804845	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs724304	0.85[CHB][hapmap]
rs726610	0.91[TSI][hapmap]
rs7609594	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs7614148	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7616458	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs7617356	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap]
rs7618429	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs7620313	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs7627971	0.83[MEX][hapmap]
rs7632056	0.82[TSI][hapmap]
rs7634761	0.89[CEU][hapmap];0.85[CHB][hapmap]
rs7652808	0.91[TSI][hapmap]
rs7653790	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs9309981	0.85[CHB][hapmap]
rs9309982	0.85[CHB][hapmap]
rs956281	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs9833314	0.85[CHB][hapmap]
rs9838811	0.85[CHB][hapmap]
rs9864170	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs9880919	0.85[CHB][hapmap]
rs993136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs993137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap]
rs993716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1002238	chr3:85357855-85719373	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
4	nsv536619	chr3:85357855-85719373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1004254	chr3:85394816-85514910	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
6	nsv536621	chr3:85394816-85514910	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
7	nsv590904	chr3:85438564-85551403	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv590905	chr3:85438564-85797093	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv998829	chr3:85449960-85641099	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv536622	chr3:85449960-85641099	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv526621	chr3:85470642-85667683	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1009512	chr3:85472690-85533487	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
13	nsv536623	chr3:85472690-85533487	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a
14	nsv967225	chr3:85474262-85482151	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
15	nsv522784	chr3:85480724-85507231	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28655875	PTCD2	trans	cerebellum	SCAN

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

No data

Quick Search:

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links