Variant report

Variant	rs2251660
Chromosome Location	chr17:34252537-34252538
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RDM1-2	chr17:34252519-34252641	NR_027996
2	lnc-RDM1-2	chr17:34252519-34252641	NR_028000

Extended variants
information (count: 126 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs11080360	0.90[ASN][1000 genomes]
rs11080361	0.90[ASN][1000 genomes]
rs11080362	0.90[ASN][1000 genomes]
rs11650409	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11652536	0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11653016	0.90[ASN][1000 genomes]
rs11653051	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11653204	0.89[ASN][1000 genomes]
rs11654713	0.87[ASN][1000 genomes]
rs11655533	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11656556	0.89[ASN][1000 genomes]
rs11657908	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11868801	0.90[ASN][1000 genomes]
rs11869976	0.90[ASN][1000 genomes]
rs16971670	0.90[ASN][1000 genomes]
rs2107538	0.92[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2107540	0.89[ASN][1000 genomes]
rs2280787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291299	0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs2376287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2526327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2526328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2702947	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2702948	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2735475	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28550999	0.90[ASN][1000 genomes]
rs28722787	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28739295	0.89[ASN][1000 genomes]
rs28912068	0.86[ASN][1000 genomes]
rs34369685	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3760447	0.86[ASN][1000 genomes]
rs3809769	0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3817655	0.82[EUR][1000 genomes]
rs3817656	0.83[ASN][1000 genomes]
rs3826404	0.89[TSI][hapmap]
rs4251751	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs4251752	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4251791	0.80[EUR][1000 genomes]
rs4795089	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs4795090	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs4795095	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4795099	0.85[ASN][1000 genomes]
rs4795100	0.90[ASN][1000 genomes]
rs4795101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4796105	0.88[TSI][hapmap]
rs4796107	0.80[CHB][hapmap];0.87[JPT][hapmap]
rs4796108	0.88[JPT][hapmap]
rs4796112	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4796114	0.85[JPT][hapmap]
rs4796115	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4796118	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs4796119	0.86[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs4796120	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs4796123	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs4796124	0.89[ASN][1000 genomes]
rs4796125	0.89[ASN][1000 genomes]
rs4796126	0.87[ASN][1000 genomes]
rs4796127	0.89[ASN][1000 genomes]
rs4796128	0.94[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs4796130	0.90[ASN][1000 genomes]
rs4796131	0.90[ASN][1000 genomes]
rs4796133	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4796134	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4796136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4796137	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4796138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56294660	0.90[ASN][1000 genomes]
rs56344830	0.87[ASN][1000 genomes]
rs59247105	0.81[ASN][1000 genomes]
rs59338510	0.89[ASN][1000 genomes]
rs6505496	0.86[GIH][hapmap];0.96[TSI][hapmap]
rs7211393	0.86[EUR][1000 genomes]
rs7213636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7215845	0.88[EUR][1000 genomes]
rs8066406	0.89[EUR][1000 genomes]
rs9303691	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9303693	0.90[ASN][1000 genomes]
rs9754	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9789051	0.89[ASN][1000 genomes]
rs9889274	0.80[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs9889977	0.90[ASN][1000 genomes]
rs9890583	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9891064	0.90[ASN][1000 genomes]
rs9893004	0.90[ASN][1000 genomes]
rs9894314	0.90[ASN][1000 genomes]
rs9894799	0.90[ASN][1000 genomes]
rs9896265	0.89[ASN][1000 genomes]
rs9896658	0.90[ASN][1000 genomes]
rs9897665	0.90[ASN][1000 genomes]
rs9898132	0.87[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9898152	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9899215	0.90[ASN][1000 genomes]
rs9899866	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9899870	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9899881	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9900236	0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9901195	0.90[ASN][1000 genomes]
rs9901418	0.90[ASN][1000 genomes]
rs9903590	0.90[ASN][1000 genomes]
rs9904675	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs9907145	0.90[ASN][1000 genomes]
rs9907295	0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.92[ASN][1000 genomes]
rs9908011	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9908525	0.90[ASN][1000 genomes]
rs9908907	0.83[ASN][1000 genomes]
rs9908928	0.81[EUR][1000 genomes]
rs9909050	0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9911016	0.90[ASN][1000 genomes]
rs9912049	0.90[ASN][1000 genomes]
rs9912284	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9912552	0.83[ASN][1000 genomes]
rs9912571	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9912793	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9912894	0.90[ASN][1000 genomes]
rs9913488	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9913559	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9914401	0.87[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs9914468	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3380735	chr17:34246253-34271932	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1063100	chr17:34246253-34397598	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv833424	chr17:34246253-34419476	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1056950	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1059795	chr17:34246253-34442620	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv1060457	chr17:34246253-34442620	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv543320	chr17:34246253-34442620	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv949160	chr17:34246253-34442620	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2251660	RDM1	cis	parietal	SCAN
rs2251660	AMAC1	cis	cerebellum	SCAN
rs2251660	RDM1	cis	lymphoblastoid	seeQTL
rs2251660	C17orf50	cis	cerebellum	SCAN
rs2251660	RDM1	cis	Lymphoblastoid	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34244800-34256800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr17:34244800-34257000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:34245400-34255000	Weak transcription	Fetal Intestine Large	intestine
4	chr17:34245600-34257200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:34246000-34256800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr17:34246000-34256800	Weak transcription	Thymus	Thymus
7	chr17:34247200-34256800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:34247400-34257000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr17:34247600-34257000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr17:34248200-34256200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr17:34248200-34256800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:34248600-34256600	Weak transcription	K562	blood
13	chr17:34249800-34257000	Weak transcription	Fetal Muscle Leg	muscle
14	chr17:34250200-34256800	Weak transcription	A549	lung
15	chr17:34250200-34257000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr17:34250200-34257000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:34251400-34256600	Weak transcription	Fetal Thymus	thymus
18	chr17:34251400-34257000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:34251600-34256800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr17:34251600-34257000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr17:34251800-34256800	Weak transcription	Primary T cells from cord blood	blood
22	chr17:34251800-34256800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr17:34251800-34256800	Weak transcription	GM12878-XiMat	blood
24	chr17:34251800-34257000	Weak transcription	Primary B cells from cord blood	blood
25	chr17:34251800-34257000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr17:34251800-34257000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr17:34251800-34257000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr17:34252000-34256600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr17:34252000-34256600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:34252200-34253800	Weak transcription	Fetal Intestine Small	intestine
31	chr17:34252400-34257000	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links