Variant report

Variant	rs7336379
Chromosome Location	chr13:49154996-49154997
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr13:49153604-49155108	SK-N-SH	brain:	n/a	chr13:49153823-49153837 chr13:49154515-49154534 chr13:49154519-49154529 chr13:49154518-49154531 chr13:49154517-49154529
2	CTCF	chr13:49154880-49155030	BE2_C	brain:	n/a	n/a
3	MAX	chr13:49154919-49155118	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr13:49154277-49155091	SK-N-SH	brain:	n/a	chr13:49154517-49154535

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RCBTB2-3	chr13:49154977-49155037	NONHSAT033722

Variant related genes	Relation type
LINC00462	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11148110	0.86[EUR][1000 genomes]
rs12877288	0.80[EUR][1000 genomes]
rs12877954	0.87[EUR][1000 genomes]
rs1359688	0.90[EUR][1000 genomes]
rs1536396	0.86[EUR][1000 genomes]
rs1536397	0.87[EUR][1000 genomes]
rs1808060	0.82[EUR][1000 genomes]
rs1887152	0.82[EUR][1000 genomes]
rs1887154	0.83[EUR][1000 genomes]
rs2104532	0.88[EUR][1000 genomes]
rs2406935	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407093	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2407095	0.88[EUR][1000 genomes]
rs2897588	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4497565	0.83[EUR][1000 genomes]
rs4635233	0.88[EUR][1000 genomes]
rs7139578	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7329065	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7332322	0.84[EUR][1000 genomes]
rs7333360	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8002098	0.88[EUR][1000 genomes]
rs9316382	0.83[EUR][1000 genomes]
rs9316394	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9316395	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9316399	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs943278	0.83[EUR][1000 genomes]
rs943280	0.90[EUR][1000 genomes]
rs943283	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526479	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526481	0.87[EUR][1000 genomes]
rs9526483	0.86[EUR][1000 genomes]
rs9535035	0.83[EUR][1000 genomes]
rs9535038	0.87[EUR][1000 genomes]
rs9535042	0.87[EUR][1000 genomes]
rs9535043	0.85[EUR][1000 genomes]
rs9535045	0.88[EUR][1000 genomes]
rs9535046	0.87[EUR][1000 genomes]
rs9535049	0.80[EUR][1000 genomes]
rs9535059	0.82[AFR][1000 genomes]
rs9568043	0.82[EUR][1000 genomes]
rs9568047	0.82[EUR][1000 genomes]
rs9568049	0.87[EUR][1000 genomes]
rs9568050	0.87[EUR][1000 genomes]
rs9568059	0.82[AFR][1000 genomes]
rs9568069	0.82[AFR][1000 genomes]
rs9595937	0.92[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9634680	0.88[EUR][1000 genomes]
rs964413	0.82[AFR][1000 genomes]
rs990814	0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7336379	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49135000-49155000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:49146800-49157400	Weak transcription	HSMMtube	muscle
3	chr13:49147600-49160800	Weak transcription	Thymus	Thymus
4	chr13:49148400-49158400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr13:49148400-49159000	Weak transcription	Pancreas	Pancrea
6	chr13:49148400-49160600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr13:49148800-49157800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr13:49150600-49159400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr13:49152400-49155000	Enhancers	Dnd41	blood
10	chr13:49152600-49155000	Enhancers	Brain Anterior Caudate	brain
11	chr13:49152600-49155400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr13:49152800-49155000	Enhancers	HepG2	liver
13	chr13:49152800-49155200	Enhancers	Brain Hippocampus Middle	brain
14	chr13:49152800-49155400	Enhancers	HMEC	breast
15	chr13:49153200-49155000	Enhancers	Stomach Mucosa	stomach
16	chr13:49153200-49155200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:49153400-49155000	Enhancers	Brain Cingulate Gyrus	brain
18	chr13:49153400-49158200	Weak transcription	Fetal Lung	lung
19	chr13:49153600-49155000	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr13:49153800-49155000	Enhancers	Brain Substantia Nigra	brain
21	chr13:49154000-49155000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr13:49154000-49155400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr13:49154000-49156800	Enhancers	GM12878-XiMat	blood
24	chr13:49154000-49158000	Weak transcription	Fetal Muscle Leg	muscle
25	chr13:49154000-49158800	Weak transcription	Right Atrium	heart
26	chr13:49154000-49159000	Weak transcription	Colonic Mucosa	Colon
27	chr13:49154000-49159000	Weak transcription	Esophagus	oesophagus
28	chr13:49154000-49159000	Weak transcription	Left Ventricle	heart
29	chr13:49154000-49159000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr13:49154000-49159000	Weak transcription	Spleen	Spleen
31	chr13:49154000-49159200	Weak transcription	Placenta	Placenta
32	chr13:49154200-49156000	Weak transcription	Fetal Intestine Small	intestine
33	chr13:49154200-49158000	Weak transcription	Adipose Nuclei	Adipose
34	chr13:49154200-49158600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr13:49154200-49159000	Weak transcription	NHEK	skin
36	chr13:49154200-49159400	Weak transcription	Fetal Thymus	thymus
37	chr13:49154200-49160800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr13:49154200-49160800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr13:49154400-49158800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:49154400-49160200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr13:49154600-49155000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
42	chr13:49154600-49155000	Enhancers	Colon Smooth Muscle	Colon
43	chr13:49154600-49155200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr13:49154600-49155400	Enhancers	Osteobl	bone
45	chr13:49154600-49159400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr13:49154800-49156000	Weak transcription	HSMM	muscle
47	chr13:49154800-49157800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr13:49154800-49158400	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr13:49154800-49158800	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr13:49154800-49158800	Weak transcription	Monocytes-CD14+_RO01746	blood

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