Variant report

Variant	rs11653282
Chromosome Location	chr17:34236746-34236747
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:34232786..34236982-chr17:34237084..34241613,5	K562	blood:
2	chr17:34236497..34238510-chr17:34243558..34246809,3	K562	blood:
3	chr17:34135239..34137919-chr17:34235430..34238099,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RDM1-1	chr17:34233172-34236953	ENSG00000248695
2	lnc-RDM1-1	chr17:34233172-34238027	ENSG00000266999.1

Variant related genes	Relation type
ENSG00000267578	Chromatin interaction
ENSG00000172660	Chromatin interaction
ENSG00000266972	Chromatin interaction
ENSG00000266999	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs11080360	0.89[EUR][1000 genomes]
rs11080361	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11080362	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11080363	0.85[CEU][hapmap]
rs11650409	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11650668	0.81[ASN][1000 genomes]
rs11652536	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11653016	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11653051	1.00[CEU][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11653204	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11654713	0.84[EUR][1000 genomes]
rs11655533	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11656556	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11657908	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11868244	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11868785	0.85[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs11868801	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11869976	0.88[EUR][1000 genomes]
rs11871113	0.82[CEU][hapmap]
rs16971670	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2107538	0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[ASN][1000 genomes]
rs2107540	0.85[EUR][1000 genomes]
rs2280789	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291299	0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs2306630	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28550999	0.85[EUR][1000 genomes]
rs28595279	0.82[ASN][1000 genomes]
rs28739295	0.85[EUR][1000 genomes]
rs28912068	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3760327	0.85[ASN][1000 genomes]
rs3760447	0.84[AMR][1000 genomes]
rs3785764	0.85[CEU][hapmap]
rs3809769	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3817655	0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.89[ASN][1000 genomes]
rs4079183	0.85[ASN][1000 genomes]
rs4251702	0.87[CEU][hapmap];0.95[TSI][hapmap]
rs4251703	0.85[JPT][hapmap]
rs4251719	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[ASN][1000 genomes]
rs4251724	0.91[JPT][hapmap]
rs4251737	0.87[ASN][1000 genomes]
rs4251749	0.80[ASN][1000 genomes]
rs4251751	0.87[CEU][hapmap]
rs4251752	0.87[CEU][hapmap]
rs4251769	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4251787	0.85[ASN][1000 genomes]
rs4251791	0.80[ASN][1000 genomes]
rs4325615	0.82[ASN][1000 genomes]
rs4795087	0.81[CHB][hapmap]
rs4795089	0.87[CEU][hapmap];0.95[TSI][hapmap]
rs4795090	0.91[JPT][hapmap]
rs4795093	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4795095	0.87[CEU][hapmap]
rs4795096	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795097	0.81[EUR][1000 genomes]
rs4795099	0.85[AMR][1000 genomes]
rs4795100	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4796107	0.87[CEU][hapmap];0.95[TSI][hapmap]
rs4796108	1.00[CEU][hapmap]
rs4796112	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs4796115	0.87[CEU][hapmap]
rs4796116	0.83[ASN][1000 genomes]
rs4796118	0.89[GIH][hapmap];0.95[TSI][hapmap]
rs4796119	0.85[CEU][hapmap];0.95[TSI][hapmap]
rs4796120	0.87[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs4796123	0.84[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4796124	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4796125	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4796126	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4796127	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4796128	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4796129	0.80[EUR][1000 genomes]
rs4796130	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4796131	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55950249	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56294660	0.85[EUR][1000 genomes]
rs56344830	0.84[EUR][1000 genomes]
rs59338510	0.83[EUR][1000 genomes]
rs6505496	0.91[JPT][hapmap]
rs7211393	0.93[ASN][1000 genomes]
rs7215845	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8080959	0.81[ASN][1000 genomes]
rs9303691	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs9303692	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9303693	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9789051	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9889274	1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9889874	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9889977	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9891064	0.89[EUR][1000 genomes]
rs9893004	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9894314	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9894799	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9896265	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9896658	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9897665	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9898132	0.87[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap]
rs9898152	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs9899215	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9899866	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs9899870	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs9900236	1.00[CEU][hapmap];0.89[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9900563	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9901195	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9901418	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9903590	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9904675	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs9907145	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9907295	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs9908011	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9908525	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9908928	0.86[ASN][1000 genomes]
rs9909050	0.87[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs9909416	0.88[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9911016	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9912049	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9912284	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9912552	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9912571	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9912793	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9912894	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9913488	1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9914401	0.87[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs9914468	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11653282	RDM1	cis	lymphoblastoid	seeQTL
rs11653282	CCL5	cis	lymphoblastoid	seeQTL
rs11653282	RDM1	cis	multi-tissue	Pritchard
rs11653282	TAF15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:34229200-34236800	Weak transcription	K562	blood
2	chr17:34229800-34240000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:34230000-34245400	Weak transcription	Primary T cells from cord blood	blood
4	chr17:34234200-34240000	Weak transcription	Fetal Intestine Large	intestine
5	chr17:34234600-34237000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:34234600-34240000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr17:34234600-34244400	Weak transcription	Thymus	Thymus
8	chr17:34234600-34251200	Weak transcription	Fetal Thymus	thymus
9	chr17:34236600-34237000	Enhancers	Fetal Intestine Small	intestine

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