Variant report

Variant	rs4938870
Chromosome Location	chr11:57306698-57306699
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10896623	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12277281	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3758921	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3851118	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4939148	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7109985	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7110678	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7925116	0.87[AMR][1000 genomes];0.91[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4938870	SMTNL1	cis	Artery Tibial	GTEx
rs4938870	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs4938870	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs4938870	TIMM10	cis	lung	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	chr11:57299400-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr11:57299400-57313600	Weak transcription	Liver	Liver
17	chr11:57299400-57314000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:57299400-57314000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr11:57299400-57314000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr11:57299400-57314000	Weak transcription	GM12878-XiMat	blood
21	chr11:57299400-57314200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:57299400-57317200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:57299600-57306800	Weak transcription	NHEK	skin
24	chr11:57299800-57306800	Weak transcription	Dnd41	blood
25	chr11:57300000-57310600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr11:57300000-57313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:57304600-57306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:57304600-57306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr11:57304600-57307000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:57304800-57314800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr11:57305000-57310000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr11:57305000-57310200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr11:57305200-57310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:57305400-57307400	Active TSS	Fetal Muscle Trunk	muscle
35	chr11:57305400-57310000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:57305400-57310000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr11:57305400-57310400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr11:57305400-57310400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr11:57305400-57310600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:57305600-57310600	Weak transcription	Fetal Stomach	stomach
41	chr11:57305800-57306800	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr11:57305800-57307400	Strong transcription	Spleen	Spleen
43	chr11:57305800-57307800	Strong transcription	Primary T cells from cord blood	blood
44	chr11:57306000-57310600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:57306000-57313600	Weak transcription	Lung	lung
46	chr11:57306000-57315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:57306200-57306800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
48	chr11:57306200-57307200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr11:57306200-57308000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:57306200-57310000	Weak transcription	H1 Cell Line	embryonic stem cell

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