Variant report

Variant	rs6739468
Chromosome Location	chr2:46849380-46849381
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46849308..46851947-chr2:46857219..46859280,2	K562	blood:
2	chr2:46843066..46846542-chr2:46848509..46851651,4	K562	blood:
3	chr2:46842719..46845147-chr2:46846797..46849881,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119878	Chromatin interaction
ENSG00000151665	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1080871	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11894342	0.87[AMR][1000 genomes]
rs12104572	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13000706	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13385693	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1451156	0.90[ASN][1000 genomes]
rs1531133	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1598517	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1989720	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242033	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3087822	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6544906	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6544907	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6739397	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6752882	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7598578	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[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
rs6739468	CRIPT	cis	Stomach	GTEx
rs6739468	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs6739468	CRIPT	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844800-46865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:46844800-46868400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:46844800-46868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:46844800-46868800	Weak transcription	Esophagus	oesophagus
5	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
6	chr2:46845200-46850000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:46845200-46854000	Weak transcription	Colonic Mucosa	Colon
8	chr2:46845400-46854000	Weak transcription	Small Intestine	intestine
9	chr2:46845400-46858400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:46845400-46864800	Weak transcription	Psoas Muscle	Psoas
11	chr2:46845400-46867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
13	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
14	chr2:46845600-46850000	Weak transcription	Fetal Heart	heart
15	chr2:46845600-46854800	Weak transcription	NHEK	skin
16	chr2:46845600-46868200	Weak transcription	Aorta	Aorta
17	chr2:46845600-46868800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:46845800-46849800	Weak transcription	HMEC	breast
19	chr2:46845800-46850000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr2:46846000-46849400	Strong transcription	Osteobl	bone
21	chr2:46846000-46854400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:46846000-46868600	Weak transcription	Fetal Intestine Small	intestine
23	chr2:46846200-46849400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:46846200-46853400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:46846200-46855200	Strong transcription	Liver	Liver
26	chr2:46846200-46857400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr2:46846400-46853400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr2:46846400-46853600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:46846400-46853800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:46846400-46853800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:46846400-46853800	Strong transcription	Placenta	Placenta
32	chr2:46846400-46856000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:46846400-46857800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr2:46846800-46849400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:46846800-46849400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:46846800-46849400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr2:46846800-46849400	Strong transcription	HSMM	muscle
38	chr2:46846800-46849800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:46846800-46850200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:46846800-46850800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr2:46846800-46850800	Strong transcription	Fetal Brain Female	brain
42	chr2:46846800-46851800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr2:46846800-46853400	Strong transcription	Brain Anterior Caudate	brain
44	chr2:46846800-46853400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:46846800-46853600	Strong transcription	NH-A	brain
46	chr2:46846800-46853800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr2:46846800-46853800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:46846800-46853800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr2:46846800-46854600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr2:46846800-46854800	Strong transcription	Fetal Thymus	thymus

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