Variant report

Variant	rs514385
Chromosome Location	chr11:57306011-57306012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1124942	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12223229	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2234409	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2467328	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2467329	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2467330	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581930	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2649644	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2649645	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2649649	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2649651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2649653	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2649655	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2649656	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2649658	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2649659	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2649666	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2729358	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729359	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2729367	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729368	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2729369	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729370	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2729375	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2729382	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848621	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848622	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2848624	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848638	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2848639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs722823	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1051032	chr11:57290124-57363064	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv541049	chr11:57290124-57363064	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1052073	chr11:57297499-57362802	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv541050	chr11:57297499-57362802	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs514385	TIMM10	cis	multi-tissue	Pritchard
rs514385	SMTNL1	cis	lung	GTEx
rs514385	UBE2L6	cis	parietal	SCAN
rs514385	OR5J2	cis	parietal	SCAN
rs514385	DTX4	cis	cerebellum	SCAN
rs514385	SLC43A1	cis	parietal	SCAN
rs514385	SLC43A3	cis	cerebellum	SCAN
rs514385	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs514385	SMTNL1	cis	Nerve Tibial	GTEx
rs514385	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs514385	SMTNL1	cis	Esophagus Muscularis	GTEx
rs514385	SMTNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs514385	SMTNL1	cis	Artery Tibial	GTEx
rs514385	TIMM10	cis	Lymphoblastoid	GTEx
rs514385	SMTNL1	cis	Thyroid	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57298800-57319200	Weak transcription	Small Intestine	intestine
2	chr11:57299000-57310200	Weak transcription	Right Ventricle	heart
3	chr11:57299000-57314000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:57299000-57317000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr11:57299000-57317200	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:57299000-57317400	Weak transcription	Fetal Brain Male	brain
7	chr11:57299200-57307000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:57299200-57307000	Weak transcription	Thymus	Thymus
9	chr11:57299200-57313600	Weak transcription	Fetal Thymus	thymus
10	chr11:57299200-57314200	Weak transcription	Brain Hippocampus Middle	brain
11	chr11:57299200-57314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:57299200-57316200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr11:57299200-57317200	Weak transcription	Brain Angular Gyrus	brain
14	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
15	chr11:57299400-57306200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:57299400-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr11:57299400-57313600	Weak transcription	Liver	Liver
18	chr11:57299400-57314000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr11:57299400-57314000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr11:57299400-57314000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:57299400-57314000	Weak transcription	GM12878-XiMat	blood
22	chr11:57299400-57314200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr11:57299400-57317200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:57299600-57306800	Weak transcription	NHEK	skin
25	chr11:57299800-57306800	Weak transcription	Dnd41	blood
26	chr11:57300000-57310600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr11:57300000-57313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:57300200-57306400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:57304400-57306400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr11:57304600-57306400	Enhancers	Psoas Muscle	Psoas
31	chr11:57304600-57306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:57304600-57306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr11:57304600-57307000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:57304800-57314800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:57305000-57310000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:57305000-57310200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr11:57305200-57306400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:57305200-57306400	Strong transcription	Brain Germinal Matrix	brain
39	chr11:57305200-57310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr11:57305400-57306200	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr11:57305400-57307400	Active TSS	Fetal Muscle Trunk	muscle
42	chr11:57305400-57310000	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:57305400-57310000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr11:57305400-57310400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:57305400-57310400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:57305400-57310600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr11:57305600-57306400	Strong transcription	Fetal Brain Female	brain
48	chr11:57305600-57310600	Weak transcription	Fetal Stomach	stomach
49	chr11:57305800-57306600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr11:57305800-57306800	Flanking Active TSS	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links