Variant report

Variant	rs2958713
Chromosome Location	chr11:3986506-3986507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10742189	0.81[EUR][1000 genomes]
rs10742223	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10767706	0.82[JPT][hapmap]
rs10767807	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs10835301	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11030224	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.80[EUR][1000 genomes]
rs11030264	0.93[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11030394	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11030536	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11030608	0.82[EUR][1000 genomes]
rs11030907	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs11604649	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12419208	0.87[AFR][1000 genomes]
rs1372805	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs17193797	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2304891	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs2920139	0.87[AFR][1000 genomes]
rs2920144	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2923944	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2923945	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[EUR][1000 genomes]
rs2923948	0.84[EUR][1000 genomes]
rs2923953	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs2923956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2959056	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[EUR][1000 genomes]
rs2959065	0.84[EUR][1000 genomes]
rs2959066	0.87[AFR][1000 genomes]
rs2959070	0.82[CEU][hapmap]
rs2959075	0.89[CEU][hapmap]
rs2959077	0.86[EUR][1000 genomes]
rs2959079	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2959081	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34662040	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910863	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4910864	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61188043	0.82[AFR][1000 genomes]
rs7102508	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7116520	0.85[AFR][1000 genomes]
rs7120938	0.82[JPT][hapmap]
rs747883	0.87[AFR][1000 genomes]
rs7938196	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7945639	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];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	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
2	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
3	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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2958713	RRM1	cis	Nerve Tibial	GTEx
rs2958713	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:77 , 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	chr11:3970800-3988600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr11:3971400-3988400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr11:3972800-3988800	Weak transcription	Fetal Muscle Leg	muscle
5	chr11:3973000-3988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:3973200-3993200	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:3973200-4008400	Weak transcription	Fetal Lung	lung
8	chr11:3973600-3993800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr11:3974800-3988200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr11:3974800-3988800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr11:3975000-4006000	Weak transcription	Right Ventricle	heart
12	chr11:3975600-3988600	Weak transcription	Dnd41	blood
13	chr11:3975600-3988800	Weak transcription	Aorta	Aorta
14	chr11:3975800-3988800	Weak transcription	Esophagus	oesophagus
15	chr11:3977400-3988600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr11:3980600-3988800	Weak transcription	GM12878-XiMat	blood
17	chr11:3980600-3994200	Weak transcription	Fetal Stomach	stomach
18	chr11:3981000-3988800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:3981200-3990400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:3981600-3988800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:3981600-3993000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:3981800-3989800	Weak transcription	Osteobl	bone
23	chr11:3981800-3990800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr11:3982000-3993200	Weak transcription	NHEK	skin
25	chr11:3982200-3988800	Weak transcription	Spleen	Spleen
26	chr11:3982400-3994200	Weak transcription	Brain Anterior Caudate	brain
27	chr11:3982600-3987200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr11:3982600-3988800	Weak transcription	Primary B cells from cord blood	blood
29	chr11:3982600-3988800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:3982600-3992800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:3982600-3994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:3982600-3994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:3982600-4004400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:3982600-4005600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr11:3982600-4006000	Weak transcription	Left Ventricle	heart
36	chr11:3983200-3988800	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr11:3983600-3988000	Weak transcription	Pancreas	Pancrea
38	chr11:3983600-3988600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:3983600-3988600	Weak transcription	Lung	lung
40	chr11:3983600-3988600	Weak transcription	Stomach Smooth Muscle	stomach
41	chr11:3983600-3992000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr11:3983800-3988600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr11:3984000-3988600	Weak transcription	Adipose Nuclei	Adipose
44	chr11:3984000-3988600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr11:3984000-3988600	Weak transcription	Thymus	Thymus
46	chr11:3984000-4010400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:3984400-3986800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr11:3984400-3993000	Weak transcription	A549	lung
49	chr11:3984600-3988800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:3984800-3989000	Enhancers	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links