Variant report

Variant	rs9595945
Chromosome Location	chr13:49201555-49201556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1009717	0.82[ASN][1000 genomes]
rs1009718	0.82[ASN][1000 genomes]
rs11840006	0.85[ASN][1000 genomes]
rs12867213	0.83[ASN][1000 genomes]
rs12874937	0.83[ASN][1000 genomes]
rs1323556	0.88[ASN][1000 genomes]
rs1575464	0.88[ASN][1000 genomes]
rs1575465	0.88[ASN][1000 genomes]
rs1575920	0.82[ASN][1000 genomes]
rs1854017	0.82[ASN][1000 genomes]
rs2406937	0.82[ASN][1000 genomes]
rs2406938	0.83[ASN][1000 genomes]
rs2406939	0.83[ASN][1000 genomes]
rs2407246	0.88[ASN][1000 genomes]
rs2897623	0.88[ASN][1000 genomes]
rs3945837	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4451857	0.82[ASN][1000 genomes]
rs4942769	0.90[ASN][1000 genomes]
rs6561469	0.82[ASN][1000 genomes]
rs7318887	0.80[ASN][1000 genomes]
rs7323160	0.88[ASN][1000 genomes]
rs7324562	0.81[ASN][1000 genomes]
rs7332030	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7990619	0.82[ASN][1000 genomes]
rs7990660	0.82[ASN][1000 genomes]
rs8000783	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8001736	0.83[ASN][1000 genomes]
rs8002035	0.83[ASN][1000 genomes]
rs9535039	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap]
rs9535059	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535060	0.83[ASN][1000 genomes]
rs9562833	0.82[ASN][1000 genomes]
rs9568056	0.82[ASN][1000 genomes]
rs9568058	0.82[ASN][1000 genomes]
rs9568059	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568061	0.81[ASN][1000 genomes]
rs9568062	0.82[ASN][1000 genomes]
rs9568064	0.83[ASN][1000 genomes]
rs9568065	0.83[ASN][1000 genomes]
rs9568069	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591187	0.83[ASN][1000 genomes]
rs9595943	0.83[ASN][1000 genomes]
rs9595944	0.83[ASN][1000 genomes]
rs964413	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][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	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
2	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
3	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
4	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
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3495983	chr13:49181790-49222165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3495984	chr13:49181790-49222165	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9595945	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49196600-49201800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr13:49196800-49205600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:49197400-49202000	Enhancers	Ovary	ovary
4	chr13:49197600-49202200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr13:49197800-49202000	Enhancers	Placenta	Placenta
6	chr13:49198000-49205000	Enhancers	Fetal Intestine Large	intestine
7	chr13:49199000-49201600	Enhancers	Adipose Nuclei	Adipose
8	chr13:49199000-49202000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr13:49199000-49205000	Enhancers	Fetal Intestine Small	intestine
10	chr13:49199200-49201800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:49199400-49201600	Enhancers	Fetal Kidney	kidney
12	chr13:49199400-49201600	Enhancers	NH-A	brain
13	chr13:49199400-49201800	Enhancers	Primary hematopoietic stem cells	blood
14	chr13:49199600-49202000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:49199600-49202000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr13:49199800-49202000	Enhancers	Stomach Mucosa	stomach
17	chr13:49199800-49204200	Weak transcription	Aorta	Aorta
18	chr13:49200000-49201600	Enhancers	K562	blood
19	chr13:49200200-49203200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr13:49200200-49203200	Enhancers	HepG2	liver
21	chr13:49200400-49202000	Flanking Active TSS	Dnd41	blood
22	chr13:49200800-49201600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:49200800-49203400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr13:49201000-49202000	Enhancers	Pancreas	Pancrea
25	chr13:49201000-49207400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:49201200-49205200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:49201400-49201600	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr13:49201400-49201800	Enhancers	Fetal Heart	heart
29	chr13:49201400-49202000	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links