Variant report

Variant	rs11842190
Chromosome Location	chr13:48508592-48508593
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SUCLA2-3	chr13:48508393-48509188	NONHSAT033689

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs11148101	1.00[EUR][1000 genomes]
rs11148102	1.00[EUR][1000 genomes]
rs11148103	1.00[EUR][1000 genomes]
rs11148104	1.00[EUR][1000 genomes]
rs11148105	1.00[EUR][1000 genomes]
rs11838821	1.00[EUR][1000 genomes]
rs11840013	1.00[EUR][1000 genomes]
rs11840146	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11840694	1.00[EUR][1000 genomes]
rs11841025	1.00[EUR][1000 genomes]
rs11841089	1.00[EUR][1000 genomes]
rs11841517	1.00[EUR][1000 genomes]
rs11842654	1.00[EUR][1000 genomes]
rs12427769	1.00[EUR][1000 genomes]
rs12428098	1.00[EUR][1000 genomes]
rs12428738	1.00[EUR][1000 genomes]
rs12428782	1.00[EUR][1000 genomes]
rs12428797	1.00[EUR][1000 genomes]
rs12429895	1.00[EUR][1000 genomes]
rs12429926	1.00[EUR][1000 genomes]
rs12430608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12584124	1.00[EUR][1000 genomes]
rs12584625	1.00[EUR][1000 genomes]
rs12584738	1.00[EUR][1000 genomes]
rs12585232	1.00[EUR][1000 genomes]
rs12585517	1.00[EUR][1000 genomes]
rs12585580	1.00[EUR][1000 genomes]
rs12585766	1.00[EUR][1000 genomes]
rs12585890	1.00[EUR][1000 genomes]
rs2148247	1.00[EUR][1000 genomes]
rs2296572	1.00[EUR][1000 genomes]
rs35535367	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3742108	1.00[EUR][1000 genomes]
rs3782979	1.00[EUR][1000 genomes]
rs4477588	0.83[ASN][1000 genomes]
rs56670154	1.00[EUR][1000 genomes]
rs57530384	1.00[EUR][1000 genomes]
rs57916684	1.00[EUR][1000 genomes]
rs58080658	1.00[EUR][1000 genomes]
rs59447207	1.00[EUR][1000 genomes]
rs59776562	1.00[EUR][1000 genomes]
rs59845585	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59991172	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60398625	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60718136	1.00[EUR][1000 genomes]
rs60828855	1.00[EUR][1000 genomes]
rs61403342	1.00[EUR][1000 genomes]
rs73477042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73479175	1.00[EUR][1000 genomes]
rs73479183	1.00[EUR][1000 genomes]
rs73479186	1.00[EUR][1000 genomes]
rs73479195	1.00[EUR][1000 genomes]
rs73479199	1.00[EUR][1000 genomes]
rs73481207	1.00[EUR][1000 genomes]
rs73481217	1.00[EUR][1000 genomes]
rs73481223	1.00[EUR][1000 genomes]
rs73481228	1.00[EUR][1000 genomes]
rs73481239	1.00[EUR][1000 genomes]
rs73481250	1.00[EUR][1000 genomes]
rs73481261	1.00[EUR][1000 genomes]
rs73481266	1.00[EUR][1000 genomes]
rs73481271	1.00[EUR][1000 genomes]
rs73481288	1.00[EUR][1000 genomes]
rs73483108	1.00[EUR][1000 genomes]
rs73483122	1.00[EUR][1000 genomes]
rs73483220	1.00[EUR][1000 genomes]
rs73483277	1.00[EUR][1000 genomes]
rs73483293	1.00[EUR][1000 genomes]
rs73485326	1.00[EUR][1000 genomes]
rs73485330	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73485345	1.00[EUR][1000 genomes]
rs73485349	1.00[EUR][1000 genomes]
rs73485356	1.00[EUR][1000 genomes]
rs73487241	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73487264	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73487269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73487297	0.84[AFR][1000 genomes]
rs73489207	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73489232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73493331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73493345	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7990408	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48492200-48510800	Weak transcription	Left Ventricle	heart
2	chr13:48501000-48531200	Weak transcription	Spleen	Spleen
3	chr13:48502000-48530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:48502600-48513600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr13:48503600-48512400	Weak transcription	Aorta	Aorta
6	chr13:48503800-48513200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:48503800-48516800	Weak transcription	NHDF-Ad	bronchial
8	chr13:48504000-48513400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:48506000-48531400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr13:48506400-48508800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr13:48506400-48508800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr13:48506400-48509000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr13:48506400-48509200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr13:48506400-48509400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr13:48506600-48508800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr13:48506800-48508800	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr13:48506800-48508800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr13:48506800-48509200	Enhancers	HSMMtube	muscle
19	chr13:48506800-48509400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr13:48506800-48509600	Enhancers	HSMM	muscle
21	chr13:48506800-48522600	Weak transcription	Fetal Brain Male	brain
22	chr13:48507000-48508600	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr13:48507000-48508800	Enhancers	H1 Cell Line	embryonic stem cell
24	chr13:48507000-48508800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr13:48507200-48508800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr13:48507200-48509000	Enhancers	Dnd41	blood
27	chr13:48507200-48509600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:48507200-48510800	Weak transcription	Primary T cells from cord blood	blood
29	chr13:48507200-48524000	Weak transcription	Lung	lung
30	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
31	chr13:48507400-48508800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr13:48507400-48508800	Enhancers	NH-A	brain
33	chr13:48507400-48512200	Weak transcription	Adipose Nuclei	Adipose
34	chr13:48507600-48511400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr13:48507600-48511600	Weak transcription	A549	lung
36	chr13:48507600-48513400	Weak transcription	Fetal Lung	lung
37	chr13:48507800-48508600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr13:48507800-48508600	Enhancers	Brain Hippocampus Middle	brain
39	chr13:48507800-48509000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr13:48507800-48511800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr13:48507800-48513600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr13:48507800-48513600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr13:48507800-48515200	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr13:48507800-48515200	Weak transcription	Osteobl	bone
45	chr13:48507800-48530600	Weak transcription	Brain Angular Gyrus	brain
46	chr13:48508000-48508800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr13:48508000-48508800	Enhancers	Brain Anterior Caudate	brain
48	chr13:48508000-48511400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr13:48508000-48514000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr13:48508000-48514200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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