Variant report

Variant	rs1049273
Chromosome Location	chr11:57174584-57174585
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC43A3-1	chr11:57174427-57176222	NONHSAT021411

Extended variants
information (count: 11 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1049272	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10792094	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs10896614	0.84[EUR][1000 genomes]
rs10896615	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11606592	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs3741085	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7106575	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7121288	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1049273	SLC43A3	Cis_1M	lymphoblastoid	RTeQTL
rs1049273	DSG2	trans	lymphoblastoid	seeQTL
rs1049273	MS4A7	cis	cerebellum	SCAN
rs1049273	TIMM10	cis	parietal	SCAN
rs1049273	OR10V1	cis	parietal	SCAN
rs1049273	OR4A15	cis	cerebellum	SCAN
rs1049273	ENSG00000134802	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57167400-57188200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:57168000-57176600	Weak transcription	Fetal Intestine Large	intestine
3	chr11:57168400-57174800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr11:57168600-57174600	Weak transcription	Fetal Intestine Small	intestine
5	chr11:57169000-57174600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:57169800-57174600	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:57170200-57174800	Weak transcription	Pancreas	Pancrea
8	chr11:57170200-57191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:57170400-57174600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:57170400-57174800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:57170400-57175000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:57170400-57176200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:57170800-57174600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:57170800-57174600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:57171000-57174800	Weak transcription	Osteobl	bone
16	chr11:57171000-57184800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr11:57171200-57175000	Weak transcription	Ovary	ovary
18	chr11:57171200-57175200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr11:57171600-57174600	Weak transcription	Fetal Lung	lung
20	chr11:57171600-57174800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:57171800-57174600	Strong transcription	Liver	Liver
22	chr11:57171800-57177200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr11:57172000-57175000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr11:57172000-57185000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:57172200-57174600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:57172200-57174800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr11:57172200-57174800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:57172400-57174800	Enhancers	NHDF-Ad	bronchial
29	chr11:57172400-57175200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
30	chr11:57172600-57174800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr11:57172600-57178000	Strong transcription	Primary T cells from cord blood	blood
32	chr11:57172600-57178000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:57172600-57178200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr11:57172600-57178200	Genic enhancers	GM12878-XiMat	blood
35	chr11:57172600-57180000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:57172600-57189800	Strong transcription	Dnd41	blood
37	chr11:57172800-57174600	Enhancers	Left Ventricle	heart
38	chr11:57172800-57174800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:57172800-57174800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:57172800-57175000	Genic enhancers	Fetal Muscle Trunk	muscle
41	chr11:57172800-57175000	Enhancers	HUVEC	blood vessel
42	chr11:57172800-57175000	Genic enhancers	NHEK	skin
43	chr11:57172800-57175200	Enhancers	A549	lung
44	chr11:57172800-57175400	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr11:57172800-57175400	Genic enhancers	Fetal Muscle Leg	muscle
46	chr11:57172800-57178400	Strong transcription	Thymus	Thymus
47	chr11:57172800-57179200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr11:57172800-57185000	Weak transcription	NH-A	brain
49	chr11:57173000-57174600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:57173000-57174600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links