Variant report

Variant	rs2235373
Chromosome Location	chr1:209963803-209963804
allele	A/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	NR3C1	chr1:209963656-209964185	A549	lung:	n/a	chr1:209963695-209963702

No.	Distal block	Cell Line	Cell type
1	chr1:209961589..209964126-chr1:209977817..209980811,2	MCF-7	breast:
2	chr1:209961943..209965694-chr1:209969094..209971510,3	K562	blood:
3	chr1:209963000..209964602-chr1:209967269..209969654,2	K562	blood:
4	chr1:209955696..209959066-chr1:209962236..209965096,3	K562	blood:
5	chr1:209955602..209959674-chr1:209962858..209967873,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232222	TF binding region
ENSG00000162757	Chromatin interaction
ENSG00000117595	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1044516	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1160411	0.80[AFR][1000 genomes]
rs11803382	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11805830	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12070337	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403599	0.81[AFR][1000 genomes]
rs17015183	0.84[EUR][1000 genomes]
rs17015218	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17015224	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17015226	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17015259	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17317411	0.82[EUR][1000 genomes]
rs2005982	0.80[AFR][1000 genomes]
rs2013162	0.83[AFR][1000 genomes]
rs2073485	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073486	0.82[AFR][1000 genomes]
rs2073487	0.81[AFR][1000 genomes]
rs2179254	0.83[AFR][1000 genomes]
rs2235372	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2235375	0.82[AFR][1000 genomes]
rs2236907	0.80[AFR][1000 genomes]
rs2236909	0.80[AFR][1000 genomes]
rs3753518	0.95[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs41305104	0.81[EUR][1000 genomes]
rs4844895	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58637469	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6540559	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540560	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6540561	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6685182	0.83[AFR][1000 genomes]
rs6694552	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6696825	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742214	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs742215	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7522250	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550857	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7552506	0.80[AFR][1000 genomes]
rs764093	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs926346	0.97[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs926347	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs926348	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv1067914	chr1:209955818-209972979	Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2235373	TRAF3IP3	cis	Whole Blood	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209957800-209978600	Weak transcription	Spleen	Spleen
2	chr1:209958000-209971600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:209958400-209968600	Weak transcription	Lung	lung
4	chr1:209958400-209971800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:209958400-209974000	Weak transcription	Aorta	Aorta
6	chr1:209958400-209978600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:209958600-209966200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:209958600-209966600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:209958600-209967000	Genic enhancers	NHEK	skin
10	chr1:209958600-209971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:209958600-209972000	Weak transcription	Fetal Kidney	kidney
12	chr1:209958600-209978800	Weak transcription	Right Ventricle	heart
13	chr1:209959400-209965000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:209959600-209966000	Genic enhancers	Fetal Intestine Small	intestine
15	chr1:209960800-209969000	Strong transcription	Placenta	Placenta
16	chr1:209961000-209974600	Weak transcription	Right Atrium	heart
17	chr1:209961400-209966000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:209961400-209966000	Genic enhancers	Rectal Mucosa Donor 31	rectum
19	chr1:209961600-209974600	Strong transcription	Placenta Amnion	Placenta Amnion
20	chr1:209961800-209964400	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr1:209962000-209966200	Strong transcription	Pancreas	Pancrea
22	chr1:209962000-209972600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:209962200-209964400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:209962200-209965000	Strong transcription	Esophagus	oesophagus
25	chr1:209962200-209977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:209962400-209964600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:209962400-209965600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:209962400-209965800	Genic enhancers	Liver	Liver
29	chr1:209962600-209964000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:209962600-209964600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:209962800-209964600	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr1:209963000-209966600	Genic enhancers	Fetal Intestine Large	intestine
33	chr1:209963000-209978800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:209963400-209964000	Genic enhancers	Stomach Mucosa	stomach
35	chr1:209963600-209964000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:209963600-209964000	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr1:209963600-209964000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
38	chr1:209963600-209964400	Strong transcription	HUVEC	blood vessel
39	chr1:209963600-209964600	Enhancers	HepG2	liver
40	chr1:209963600-209966000	Genic enhancers	Gastric	stomach
41	chr1:209963600-209967000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:209963800-209964000	Enhancers	Fetal Heart	heart
43	chr1:209963800-209964200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:209963800-209964200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr1:209963800-209964200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:209963800-209964200	Enhancers	Colonic Mucosa	Colon
47	chr1:209963800-209964200	Genic enhancers	Left Ventricle	heart
48	chr1:209963800-209964200	Active TSS	Rectal Smooth Muscle	rectum
49	chr1:209963800-209964200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
50	chr1:209963800-209964200	Enhancers	Small Intestine	intestine

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