Variant report

Variant	rs7924984
Chromosome Location	chr11:3974588-3974589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:3973583..3975273-chr11:3982575..3984995,2	K562	blood:
2	chr11:3972776..3975865-chr11:3976108..3980315,4	K562	blood:
3	chr11:3888173..3890485-chr11:3973419..3975763,2	K562	blood:
4	chr11:3945861..3948795-chr11:3974406..3976438,2	K562	blood:

Variant related genes	Relation type
ENSG00000167323	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs1013351	0.85[EUR][1000 genomes]
rs10500590	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10742200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10767702	0.85[EUR][1000 genomes]
rs10767706	0.82[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap]
rs10767713	0.87[EUR][1000 genomes]
rs10767715	0.87[GIH][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs10767720	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10767721	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10767723	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10767767	0.87[GIH][hapmap];0.87[TSI][hapmap]
rs10767811	0.83[GIH][hapmap];0.88[TSI][hapmap]
rs10835311	0.85[EUR][1000 genomes]
rs10835312	0.83[EUR][1000 genomes]
rs10835320	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10835324	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835331	0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10835333	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835337	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10835340	0.87[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10835359	0.88[EUR][1000 genomes]
rs10835390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10835399	0.87[EUR][1000 genomes]
rs10835402	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs10835403	0.87[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs10835406	0.87[EUR][1000 genomes]
rs10835407	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10835508	0.84[YRI][hapmap];0.81[EUR][1000 genomes]
rs10835596	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs11030276	0.85[EUR][1000 genomes]
rs11030404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11030599	0.81[EUR][1000 genomes]
rs11030639	0.89[GIH][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs11030781	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs11493482	0.81[EUR][1000 genomes]
rs1155146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11828337	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12223176	0.88[EUR][1000 genomes]
rs12270732	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12281293	0.87[EUR][1000 genomes]
rs12283447	0.87[EUR][1000 genomes]
rs12286710	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs12290747	0.85[EUR][1000 genomes]
rs12295138	0.81[EUR][1000 genomes]
rs1349583	0.87[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs1452047	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs1452048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17081	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs17279635	0.87[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs1839910	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2412338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2898947	0.88[EUR][1000 genomes]
rs4910865	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910866	0.85[EUR][1000 genomes]
rs4910868	0.88[EUR][1000 genomes]
rs4910869	0.87[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs6578421	0.80[YRI][hapmap]
rs6578424	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66503725	0.88[EUR][1000 genomes]
rs66596383	0.90[EUR][1000 genomes]
rs67300156	0.86[EUR][1000 genomes]
rs7102215	0.85[EUR][1000 genomes]
rs7113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120938	0.82[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap]
rs7128762	0.85[EUR][1000 genomes]
rs7129444	0.82[GIH][hapmap]
rs720571	0.86[EUR][1000 genomes]
rs750525	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7925954	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7950153	0.84[GIH][hapmap];0.90[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs963998	0.83[GIH][hapmap];0.90[TSI][hapmap]
rs995498	0.87[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	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
6	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7924984	OR51E2	cis	cerebellum	SCAN
rs7924984	FAM160A2	cis	parietal	SCAN
rs7924984	IFITM5	cis	cerebellum	SCAN
rs7924984	RRM1	cis	multi-tissue	Pritchard
rs7924984	CD81	cis	parietal	SCAN
rs7924984	TRIM21	cis	cerebellum	SCAN
rs7924984	RRM1	cis	Artery Tibial	GTEx
rs7924984	RRM1	cis	cerebellum	SCAN
rs7924984	ANO9	cis	parietal	SCAN
rs7924984	STIM1	cis	lung	GTEx
rs7924984	RRM1	cis	Thyroid	GTEx
rs7924984	RRM1	cis	parietal	SCAN
rs7924984	OR51A4	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3961200-4002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:3961600-3975200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:3968200-3974600	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr11:3968200-3980200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:3968800-3974600	Weak transcription	HMEC	breast
6	chr11:3969000-3974600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr11:3969000-3975400	Weak transcription	NHDF-Ad	bronchial
8	chr11:3969000-3980400	Weak transcription	NHLF	lung
9	chr11:3969400-3974600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:3969400-3974600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr11:3969400-3974800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr11:3969400-3975200	Weak transcription	Aorta	Aorta
13	chr11:3969400-3975200	Weak transcription	NHEK	skin
14	chr11:3969400-3975800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:3969400-3976800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:3969400-3980000	Weak transcription	Liver	Liver
17	chr11:3969600-3974600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:3969600-3977800	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr11:3970200-3976200	Enhancers	Primary T cells fromperipheralblood	blood
20	chr11:3970200-3977200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:3970600-3976000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr11:3970600-3978000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:3970800-3974600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:3970800-3974800	Enhancers	Primary hematopoietic stem cells	blood
25	chr11:3970800-3977000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr11:3970800-3977800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr11:3970800-3988600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr11:3971200-3975600	Enhancers	Dnd41	blood
29	chr11:3971400-3975400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr11:3971400-3975400	Enhancers	Psoas Muscle	Psoas
31	chr11:3971400-3988400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr11:3971800-3974800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr11:3972000-3976200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr11:3972200-3974800	Enhancers	Right Atrium	heart
35	chr11:3972400-3975200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:3972600-3975400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:3972600-3975600	Weak transcription	Lung	lung
38	chr11:3972600-3976000	Weak transcription	GM12878-XiMat	blood
39	chr11:3972800-3979400	Weak transcription	HepG2	liver
40	chr11:3972800-3979600	Weak transcription	A549	lung
41	chr11:3972800-3988800	Weak transcription	Fetal Muscle Leg	muscle
42	chr11:3973000-3974800	Weak transcription	Placenta	Placenta
43	chr11:3973000-3975400	Genic enhancers	Fetal Thymus	thymus
44	chr11:3973000-3976200	Enhancers	Thymus	Thymus
45	chr11:3973000-3977400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr11:3973000-3977800	Enhancers	Primary T cells from cord blood	blood
47	chr11:3973000-3978000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr11:3973000-3988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr11:3973200-3974600	Weak transcription	Spleen	Spleen
50	chr11:3973200-3975200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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