Variant report

Variant	rs11030639
Chromosome Location	chr11:4039056-4039057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1013351	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs10500590	0.95[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10742200	0.83[YRI][hapmap];0.81[EUR][1000 genomes]
rs10767702	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10767713	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10767715	0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10767767	1.00[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10767811	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10835311	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10835312	0.83[EUR][1000 genomes]
rs10835331	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10835333	0.83[LWK][hapmap];0.81[TSI][hapmap]
rs10835337	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs10835340	0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs10835359	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10835390	0.80[EUR][1000 genomes]
rs10835399	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835402	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835403	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835406	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835407	0.95[CEU][hapmap];0.93[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10835454	0.88[EUR][1000 genomes]
rs10835474	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10835508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835521	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835540	0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10835545	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10835554	0.85[ASN][1000 genomes]
rs10835556	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10835557	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10835561	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835596	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835597	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835601	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835604	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10835611	0.86[CHB][hapmap]
rs11030276	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs11030404	0.89[GIH][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs11030579	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11030580	0.82[ASN][1000 genomes]
rs11030599	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11030627	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11030631	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030660	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030781	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11030918	0.87[CHD][hapmap];0.87[GIH][hapmap]
rs11031110	0.85[CHB][hapmap]
rs11493482	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12223176	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs12281293	0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs12283447	0.86[EUR][1000 genomes]
rs12286710	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes]
rs12290747	0.84[EUR][1000 genomes]
rs12295138	0.80[EUR][1000 genomes]
rs1349583	0.95[CEU][hapmap];0.93[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1442726	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1452047	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1452048	0.80[EUR][1000 genomes]
rs17081	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17279635	0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1839910	0.80[EUR][1000 genomes]
rs2119987	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412338	0.81[EUR][1000 genomes]
rs28419002	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2898947	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2923948	0.81[GIH][hapmap]
rs3817657	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs4910590	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910595	0.82[LWK][hapmap]
rs4910596	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910597	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4910598	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4910866	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4910868	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs4910869	0.91[CEU][hapmap];0.93[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910875	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910877	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4910880	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6578421	0.88[YRI][hapmap]
rs6578424	0.85[GIH][hapmap];0.82[LWK][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs66503725	0.87[EUR][1000 genomes]
rs66596383	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67065286	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67300156	0.85[EUR][1000 genomes]
rs7102215	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7113845	0.81[EUR][1000 genomes]
rs7128762	0.95[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7129444	0.93[GIH][hapmap]
rs7130580	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs714380	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720571	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs723779	0.91[YRI][hapmap]
rs750525	0.81[TSI][hapmap]
rs7924984	0.89[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs7932702	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs7935824	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940013	0.82[CHD][hapmap]
rs7950153	0.86[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs963998	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs995498	0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]

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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11030639	TRIM21	cis	cerebellum	SCAN
rs11030639	RRM1	cis	cerebellum	SCAN
rs11030639	RRM1	cis	Artery Tibial	GTEx
rs11030639	IFITM5	cis	cerebellum	SCAN
rs11030639	C11orf35	cis	parietal	SCAN
rs11030639	ANO9	cis	parietal	SCAN
rs11030639	RRM1	cis	Thyroid	GTEx
rs11030639	RRM1	cis	parietal	SCAN
rs11030639	CD81	cis	parietal	SCAN
rs11030639	OR52M1	cis	cerebellum	SCAN
rs11030639	STIM1	cis	lung	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4017400-4041400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr11:4017600-4043400	Weak transcription	Primary B cells from cord blood	blood
3	chr11:4020800-4045000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:4021000-4043600	Weak transcription	Thymus	Thymus
5	chr11:4021000-4044200	Weak transcription	Fetal Thymus	thymus
6	chr11:4021000-4044400	Weak transcription	Dnd41	blood
7	chr11:4028800-4043400	Weak transcription	Primary T cells from cord blood	blood
8	chr11:4029000-4041400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:4030200-4044800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr11:4036600-4040800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr11:4037000-4039200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr11:4037200-4045000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr11:4037400-4040000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:4037600-4039600	Enhancers	Placenta	Placenta
15	chr11:4037800-4039200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr11:4037800-4040200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr11:4038000-4039200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
18	chr11:4038000-4039200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr11:4038000-4044400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr11:4038000-4049400	Weak transcription	Spleen	Spleen
21	chr11:4038200-4039800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr11:4038200-4040000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr11:4038200-4044000	Weak transcription	GM12878-XiMat	blood
24	chr11:4038200-4048800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:4038200-4057200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:4038200-4065200	Weak transcription	Left Ventricle	heart
27	chr11:4038400-4039600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:4038400-4044000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:4038400-4045000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr11:4038400-4045000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:4038400-4045400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr11:4038400-4045400	Weak transcription	Psoas Muscle	Psoas
33	chr11:4038400-4065400	Weak transcription	Esophagus	oesophagus
34	chr11:4038600-4044000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr11:4038800-4044400	Weak transcription	Primary B cells from peripheral blood	blood
36	chr11:4038800-4045000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr11:4038800-4045000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:4038800-4050000	Weak transcription	K562	blood
39	chr11:4039000-4040200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr11:4039000-4041200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:4039000-4041200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links