Variant report

Variant	rs17754039
Chromosome Location	chr10:26978296-26978297
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDSS1-3	chr10:26978267-26978528	NONHSAT011855

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10128125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10128192	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10829048	0.96[ASN][1000 genomes]
rs11015219	0.82[YRI][hapmap]
rs11015220	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015221	0.96[AFR][1000 genomes]
rs11015226	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11015233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11015234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11816510	0.83[ASN][1000 genomes]
rs11818450	0.83[ASN][1000 genomes]
rs12242239	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12242246	0.96[AFR][1000 genomes]
rs12242414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12244725	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs12245051	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246285	0.96[ASN][1000 genomes]
rs12247299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12247597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12250220	0.82[YRI][hapmap]
rs12252298	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12252358	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12252368	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12255583	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12255942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12260035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12260298	0.96[ASN][1000 genomes]
rs12260466	0.92[ASN][1000 genomes]
rs12262082	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12262401	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12263262	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12263578	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12264509	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12264994	0.96[AFR][1000 genomes]
rs12265505	1.00[EUR][1000 genomes]
rs12265633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12265746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12266764	0.96[AFR][1000 genomes]
rs12267744	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12268014	0.96[AFR][1000 genomes]
rs12268883	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12269520	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17754051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980754	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2005120	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2477276	0.81[ASN][1000 genomes]
rs2489564	0.81[ASN][1000 genomes]
rs34314417	0.92[ASN][1000 genomes]
rs34901510	0.96[ASN][1000 genomes]
rs35534478	0.96[ASN][1000 genomes]
rs35687107	0.96[ASN][1000 genomes]
rs35827769	0.96[ASN][1000 genomes]
rs4309054	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7072558	0.82[YRI][hapmap]
rs7082973	1.00[AFR][1000 genomes]
rs7097696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72481186	1.00[AMR][1000 genomes]
rs72485013	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72485015	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72485017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72485018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72485022	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72485023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72485026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753705	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7896604	1.00[AFR][1000 genomes]
rs7899631	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7899804	0.96[AFR][1000 genomes]
rs7900674	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7906473	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7920279	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894975	chr10:26343356-27014467	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv3333006	chr10:26908323-26985227	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	esv1798973	chr10:26968171-27001814	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv550233	chr10:26968171-27011323	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:26974200-26978600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr10:26977600-26981200	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr10:26977800-26978400	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr10:26977800-26979400	Enhancers	Thymus	Thymus
5	chr10:26978000-26978800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr10:26978000-26979000	Enhancers	Dnd41	blood
7	chr10:26978200-26978600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:26978200-26978600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr10:26978200-26978800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr10:26978200-26978800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr10:26978200-26979000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr10:26978200-26980200	Enhancers	Fetal Thymus	thymus

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