Variant report

Variant	rs1989720
Chromosome Location	chr2:46854364-46854365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46854125..46858531-chr2:46860398..46864023,5	K562	blood:
2	chr2:46843158..46845887-chr2:46851789..46854759,3	K562	blood:

Variant related genes	Relation type
ENSG00000151665	Chromatin interaction
ENSG00000119878	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1080871	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894342	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12104572	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13000706	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13385693	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1451156	0.94[ASN][1000 genomes]
rs1531133	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1598517	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2242033	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3087822	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544906	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6544907	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6739397	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6739468	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6752882	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598578	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1989720	ENSG00000119878	cis	multi-tissue	Pritchard
rs1989720	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs1989720	CRIPT	cis	Stomach	GTEx
rs1989720	CRIPT	cis	multi-tissue	Pritchard
rs1989720	CRIPT	cis	Esophagus Muscularis	GTEx

Chromatin state (count:116 , 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	chr2:46845400-46858400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:46845400-46864800	Weak transcription	Psoas Muscle	Psoas
8	chr2:46845400-46867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
10	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
11	chr2:46845600-46854800	Weak transcription	NHEK	skin
12	chr2:46845600-46868200	Weak transcription	Aorta	Aorta
13	chr2:46845600-46868800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:46846000-46854400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:46846000-46868600	Weak transcription	Fetal Intestine Small	intestine
16	chr2:46846200-46855200	Strong transcription	Liver	Liver
17	chr2:46846200-46857400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:46846400-46856000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr2:46846400-46857800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:46846800-46854600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr2:46846800-46854800	Strong transcription	Fetal Thymus	thymus
22	chr2:46846800-46857200	Strong transcription	Adipose Nuclei	Adipose
23	chr2:46846800-46857800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:46846800-46858200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:46846800-46858200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:46846800-46858400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:46846800-46858400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:46846800-46858600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:46846800-46859400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:46847000-46854800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:46847000-46855200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:46847800-46854800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:46848000-46856200	Weak transcription	Gastric	stomach
34	chr2:46848400-46857200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr2:46848600-46860000	Weak transcription	NHLF	lung
36	chr2:46848600-46860600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:46848600-46861800	Weak transcription	GM12878-XiMat	blood
38	chr2:46848600-46864800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:46848600-46867400	Weak transcription	Lung	lung
40	chr2:46848600-46871200	Weak transcription	HSMMtube	muscle
41	chr2:46848600-46872600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:46848600-46872800	Weak transcription	Left Ventricle	heart
43	chr2:46848600-46872800	Weak transcription	Ovary	ovary
44	chr2:46848800-46858600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:46848800-46868000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:46848800-46871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:46848800-46872600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:46848800-46873000	Weak transcription	Brain Angular Gyrus	brain
49	chr2:46849000-46854800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:46849000-46858600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links