Variant report

Variant	rs2959081
Chromosome Location	chr11:4027040-4027041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10742189	0.89[GIH][hapmap];0.87[TSI][hapmap]
rs10742223	0.82[CHB][hapmap]
rs10767807	0.82[CHB][hapmap]
rs11030224	0.85[CEU][hapmap];0.81[CHB][hapmap]
rs11030264	0.92[CEU][hapmap]
rs11030394	0.84[EUR][1000 genomes]
rs11030536	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11030608	0.83[EUR][1000 genomes]
rs11030842	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.96[TSI][hapmap]
rs11030907	0.81[CHB][hapmap]
rs11604649	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs12364664	0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs12803023	0.93[ASW][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.87[MKK][hapmap];0.80[YRI][hapmap]
rs1372804	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap]
rs1372805	0.85[ASW][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.81[AMR][1000 genomes]
rs1662172	0.83[MEX][hapmap]
rs2304891	0.85[ASW][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap]
rs2412344	0.82[CHB][hapmap]
rs2920143	0.82[CHB][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs2920144	0.85[ASW][hapmap];0.81[MKK][hapmap]
rs2923944	0.93[ASW][hapmap];0.96[CEU][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2923945	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2923948	0.82[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2923956	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2958713	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2958714	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2959056	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2959065	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2959068	0.93[ASW][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.87[MKK][hapmap];0.80[YRI][hapmap]
rs2959070	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2959074	0.82[CHB][hapmap];0.80[YRI][hapmap];0.80[AMR][1000 genomes]
rs2959075	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2959077	0.87[EUR][1000 genomes]
rs2959079	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910863	0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs61188043	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7102508	0.81[CHB][hapmap];0.83[AMR][1000 genomes]
rs7110060	0.82[CHB][hapmap];0.85[AMR][1000 genomes]
rs7116520	0.83[AMR][1000 genomes]
rs7124301	0.85[AMR][1000 genomes]
rs7945639	0.92[CEU][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2959081	RRM1	cis	Artery Tibial	GTEx
rs2959081	OR52B4	cis	cerebellum	SCAN
rs2959081	OR51A4	cis	parietal	SCAN
rs2959081	RRM1	cis	Nerve Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3989400-4031000	Weak transcription	Aorta	Aorta
2	chr11:4011800-4027600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:4017400-4041400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:4017600-4043400	Weak transcription	Primary B cells from cord blood	blood
5	chr11:4018200-4027200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:4018800-4027200	Weak transcription	Psoas Muscle	Psoas
7	chr11:4020800-4027600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:4020800-4037600	Weak transcription	Pancreas	Pancrea
9	chr11:4020800-4045000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr11:4021000-4032200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:4021000-4043600	Weak transcription	Thymus	Thymus
12	chr11:4021000-4044200	Weak transcription	Fetal Thymus	thymus
13	chr11:4021000-4044400	Weak transcription	Dnd41	blood
14	chr11:4027000-4028200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr11:4027000-4028800	Enhancers	Primary T cells from cord blood	blood
16	chr11:4027000-4028800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:4027000-4029200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr11:4027000-4029200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr11:4027000-4029200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr11:4027000-4029600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr11:4027000-4030000	Enhancers	Skeletal Muscle Female	skeletal muscle

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