Variant report

Variant	rs2729381
Chromosome Location	chr11:57309640-57309641
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57296719..57299374-chr11:57308110..57310728,2	K562	blood:

Variant related genes	Relation type
ENSG00000134809	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs2234412	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2509896	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2649660	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2649661	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2729360	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2729361	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2729372	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2848623	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2848632	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2848633	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5847	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2729381	SMTNL1	cis	Adipose Subcutaneous	GTEx
rs2729381	SMTNL1	cis	Artery Tibial	GTEx
rs2729381	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2729381	SMTNL1	cis	Nerve Tibial	GTEx
rs2729381	SMTNL1	cis	lung	GTEx

Chromatin state (count:58 , 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	chr11:57299200-57313600	Weak transcription	Fetal Thymus	thymus
8	chr11:57299200-57314200	Weak transcription	Brain Hippocampus Middle	brain
9	chr11:57299200-57314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:57299200-57316200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr11:57299200-57317200	Weak transcription	Brain Angular Gyrus	brain
12	chr11:57299200-57333000	Weak transcription	Right Atrium	heart
13	chr11:57299400-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr11:57299400-57313600	Weak transcription	Liver	Liver
15	chr11:57299400-57314000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr11:57299400-57314000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr11:57299400-57314000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:57299400-57314000	Weak transcription	GM12878-XiMat	blood
19	chr11:57299400-57314200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr11:57299400-57317200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:57300000-57310600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:57300000-57313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:57304800-57314800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr11:57305000-57310000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:57305000-57310200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:57305200-57310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:57305400-57310000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:57305400-57310000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr11:57305400-57310400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr11:57305400-57310400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr11:57305400-57310600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr11:57305600-57310600	Weak transcription	Fetal Stomach	stomach
33	chr11:57306000-57310600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:57306000-57313600	Weak transcription	Lung	lung
35	chr11:57306000-57315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr11:57306200-57310000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr11:57306400-57310000	Weak transcription	Brain Germinal Matrix	brain
38	chr11:57306400-57310400	Weak transcription	Fetal Brain Female	brain
39	chr11:57306800-57315000	Weak transcription	Gastric	stomach
40	chr11:57307200-57309800	Enhancers	Fetal Muscle Leg	muscle
41	chr11:57307200-57314600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr11:57307200-57333600	Weak transcription	HMEC	breast
43	chr11:57307400-57310000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr11:57307400-57313200	Weak transcription	Dnd41	blood
45	chr11:57307400-57313400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr11:57307400-57313400	Weak transcription	Spleen	Spleen
47	chr11:57307400-57314000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr11:57307400-57314600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr11:57307600-57313000	Weak transcription	Thymus	Thymus
50	chr11:57307600-57313600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links