Variant report

Variant	rs11842662
Chromosome Location	chr13:49160927-49160928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10076	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs10467381	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11840819	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11842402	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13378245	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17071695	1.00[CHD][hapmap]
rs17071917	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17071960	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs174854	0.90[AMR][1000 genomes]
rs174858	1.00[CHD][hapmap]
rs198565	0.90[AMR][1000 genomes]
rs198573	0.90[AMR][1000 genomes]
rs198581	0.85[AMR][1000 genomes]
rs198583	0.90[AMR][1000 genomes]
rs198587	0.90[AMR][1000 genomes]
rs2804088	0.82[MEX][hapmap]
rs2984828	0.90[AMR][1000 genomes]
rs3020646	1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs411862	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs4151590	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs449268	1.00[CHD][hapmap]
rs7322110	0.95[AMR][1000 genomes]
rs7332631	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7984270	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316386	1.00[CHD][hapmap]
rs9316392	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs9316396	1.00[CHD][hapmap]
rs9316403	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9332025	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9332036	0.95[AMR][1000 genomes]
rs9332050	0.90[AMR][1000 genomes]
rs9332053	0.83[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes]
rs9332066	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs9591167	0.95[AMR][1000 genomes]
rs9591170	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591171	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9591174	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591175	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595913	0.90[AMR][1000 genomes]
rs9595917	0.95[AMR][1000 genomes]
rs9595930	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11842662	RCBTB2	cis	lymphoblastoid	seeQTL
rs11842662	DDX6	trans	brain	seeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49156000-49161400	Enhancers	HepG2	liver
2	chr13:49156400-49161400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:49157400-49161200	Enhancers	HSMMtube	muscle
4	chr13:49157600-49164800	Weak transcription	Gastric	stomach
5	chr13:49157800-49161200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:49158000-49161400	Enhancers	Colon Smooth Muscle	Colon
7	chr13:49158000-49161600	Enhancers	HMEC	breast
8	chr13:49158000-49161600	Enhancers	HUVEC	blood vessel
9	chr13:49158200-49161000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:49158200-49161000	Enhancers	Osteobl	bone
11	chr13:49158200-49161400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr13:49158400-49161200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr13:49158600-49161000	Enhancers	Brain Germinal Matrix	brain
14	chr13:49158600-49161200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:49158600-49161200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:49158600-49161200	Enhancers	Brain Cingulate Gyrus	brain
17	chr13:49158600-49161200	Enhancers	Stomach Mucosa	stomach
18	chr13:49158600-49161400	Enhancers	Adipose Nuclei	Adipose
19	chr13:49158600-49161400	Enhancers	Fetal Muscle Leg	muscle
20	chr13:49158800-49161000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:49158800-49161200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr13:49158800-49161400	Enhancers	Brain Angular Gyrus	brain
23	chr13:49158800-49161400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr13:49158800-49161400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr13:49158800-49161400	Enhancers	Rectal Smooth Muscle	rectum
26	chr13:49158800-49161400	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr13:49159000-49161000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:49159000-49161000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr13:49159000-49162200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr13:49159200-49161000	Enhancers	HSMM	muscle
31	chr13:49159200-49161200	Enhancers	Fetal Lung	lung
32	chr13:49159200-49161400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr13:49159200-49161400	Enhancers	Brain Substantia Nigra	brain
34	chr13:49159200-49161400	Enhancers	Duodenum Mucosa	Duodenum
35	chr13:49159200-49163400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr13:49159400-49161000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr13:49159400-49161200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr13:49159400-49161200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr13:49159400-49161200	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr13:49159400-49161600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr13:49159600-49161000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr13:49159600-49161200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr13:49159600-49161200	Enhancers	Fetal Heart	heart
44	chr13:49159600-49161400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr13:49159600-49161600	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr13:49159600-49161600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr13:49159600-49161800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
48	chr13:49159600-49162400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr13:49159800-49161200	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr13:49159800-49161400	Enhancers	Primary T helper cells fromperipheralblood	blood

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