Variant report

Variant	rs9868263
Chromosome Location	chr3:53164094-53164095
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75589741..75590246-chr3:53163554..53164394,2	Hela-S3	cervix:
2	chr3:53160337..53170540-chr3:53189028..53198029,25	MCF-7	breast:
3	chr3:53163608..53165597-chr3:53189002..53191742,3	K562	blood:
4	chr3:53163489..53166052-chr3:53379929..53382792,2	K562	blood:
5	chr11:93474325..93475060-chr3:53163950..53164468,2	Hela-S3	cervix:
6	chr14:23564479..23565041-chr3:53163877..53164468,2	Hela-S3	cervix:
7	chr3:53163023..53165298-chr3:53287497..53290275,3	K562	blood:

Variant related genes	Relation type
ENSG00000166012	Chromatin interaction
ENSG00000162290	Chromatin interaction
ENSG00000182919	Chromatin interaction
ENSG00000163931	Chromatin interaction
ENSG00000205084	Chromatin interaction
ENSG00000179933	Chromatin interaction
ENSG00000163932	Chromatin interaction
ENSG00000100813	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11130341	0.87[EUR][1000 genomes]
rs12630819	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12638996	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13319872	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13433700	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1560332	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2564929	0.91[ASN][1000 genomes]
rs2564944	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28501212	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28734933	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796351	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4282053	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687570	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55950520	0.91[ASN][1000 genomes]
rs56058643	0.91[ASN][1000 genomes]
rs56386026	0.91[ASN][1000 genomes]
rs57261253	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57514626	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61296683	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255925	0.91[ASN][1000 genomes]
rs62255926	0.83[ASN][1000 genomes]
rs62255929	0.91[ASN][1000 genomes]
rs62255931	0.91[ASN][1000 genomes]
rs6445565	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445566	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769931	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769944	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6777975	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6783748	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6784207	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792345	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792363	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799837	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6809973	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73088322	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73088327	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73088342	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7615099	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs891369	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9757079	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817467	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9820125	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820324	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824325	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9828221	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834111	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838517	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844531	0.88[EUR][1000 genomes]
rs9845021	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9845352	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9845484	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9858469	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9861744	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9867023	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867590	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9868406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872260	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878875	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590356	chr3:53134098-53170500	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	nsv460553	chr3:53147576-53185061	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv590357	chr3:53147576-53185061	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
4	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9868263	RFT1	cis	Esophagus Muscularis	GTEx
rs9868263	SERBP1P3	cis	Thyroid	GTEx
rs9868263	RFT1	cis	Artery Aorta	GTEx
rs9868263	RFT1	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53163200-53164200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:53163200-53164400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr3:53163400-53164200	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr3:53163400-53164200	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr3:53163400-53164200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:53163400-53164200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:53163400-53164800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:53163400-53165000	Active TSS	Fetal Muscle Trunk	muscle
9	chr3:53163400-53165200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:53163400-53165200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:53163400-53165200	Active TSS	GM12878-XiMat	blood
12	chr3:53163600-53164200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
13	chr3:53163600-53164200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr3:53163600-53164200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
15	chr3:53163600-53164200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr3:53163600-53164200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:53163600-53164200	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr3:53163600-53164600	Active TSS	Colonic Mucosa	Colon
19	chr3:53163600-53164800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:53163600-53164800	Active TSS	H1 Cell Line	embryonic stem cell
21	chr3:53163600-53164800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:53163600-53164800	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr3:53163600-53164800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:53163600-53164800	Active TSS	Fetal Intestine Large	intestine
25	chr3:53163600-53164800	Active TSS	A549	lung
26	chr3:53163600-53165000	Active TSS	H9 Cell Line	embryonic stem cell
27	chr3:53163600-53165000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:53163600-53165000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:53163600-53165000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:53163600-53165000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:53163600-53165000	Active TSS	Esophagus	oesophagus
32	chr3:53163600-53165000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr3:53163600-53165000	Active TSS	Left Ventricle	heart
34	chr3:53163600-53165000	Active TSS	Lung	lung
35	chr3:53163600-53165000	Active TSS	Ovary	ovary
36	chr3:53163600-53165000	Active TSS	Pancreas	Pancrea
37	chr3:53163600-53165000	Active TSS	Psoas Muscle	Psoas
38	chr3:53163600-53165000	Active TSS	Right Atrium	heart
39	chr3:53163600-53165200	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr3:53163800-53164200	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr3:53163800-53164200	Bivalent/Poised TSS	HepG2	liver
42	chr3:53163800-53164600	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr3:53163800-53164600	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr3:53163800-53164600	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr3:53163800-53164600	Active TSS	Muscle Satellite Cultured Cells	--
46	chr3:53163800-53164600	Active TSS	NHEK	skin
47	chr3:53163800-53164800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:53163800-53164800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:53163800-53164800	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr3:53163800-53164800	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links