Variant report

Variant	rs6724790
Chromosome Location	chr2:46870757-46870758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs13385693	0.81[ASN][1000 genomes]
rs6544907	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6724790	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs6724790	CRIPT	cis	Stomach	GTEx
rs6724790	CRIPT	cis	Esophagus Muscularis	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
2	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
3	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
4	chr2:46848600-46871200	Weak transcription	HSMMtube	muscle
5	chr2:46848600-46872600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:46848600-46872800	Weak transcription	Left Ventricle	heart
7	chr2:46848600-46872800	Weak transcription	Ovary	ovary
8	chr2:46848800-46871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:46848800-46872600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:46848800-46873000	Weak transcription	Brain Angular Gyrus	brain
11	chr2:46849000-46877200	Weak transcription	Brain Substantia Nigra	brain
12	chr2:46849200-46870800	Weak transcription	Hela-S3	cervix
13	chr2:46849200-46872600	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:46849400-46872800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:46852000-46872800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:46853400-46872600	Weak transcription	Brain Anterior Caudate	brain
17	chr2:46853400-46872800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:46853800-46873000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:46854400-46871800	Weak transcription	Fetal Lung	lung
20	chr2:46854800-46872800	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:46854800-46878600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:46857200-46871800	Weak transcription	Adipose Nuclei	Adipose
23	chr2:46858000-46874800	Weak transcription	Liver	Liver
24	chr2:46860400-46871000	Weak transcription	NHDF-Ad	bronchial
25	chr2:46862400-46877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr2:46866800-46871000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr2:46867600-46872800	Weak transcription	Lung	lung
28	chr2:46869200-46871200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:46869200-46871400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
30	chr2:46869200-46871800	Weak transcription	Fetal Stomach	stomach
31	chr2:46869400-46871000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr2:46869400-46883400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:46869600-46871400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:46869600-46872000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:46869600-46872400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:46869600-46876800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:46869600-46881200	Weak transcription	Primary T cells from cord blood	blood
38	chr2:46869800-46870800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:46869800-46870800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:46869800-46870800	Weak transcription	Osteobl	bone
41	chr2:46869800-46871000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:46869800-46871800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:46869800-46872200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:46869800-46873000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr2:46869800-46878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:46869800-46882200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:46870000-46870800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:46870000-46871000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:46870000-46871800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:46870000-46871800	Weak transcription	NH-A	brain

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