Variant report

Variant	rs10803853
Chromosome Location	chr2:171788459-171788460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:171764593..171767413-chr2:171787705..171789524,2	K562	blood:
2	chr2:171788393..171792186-chr2:171793028..171799958,7	MCF-7	breast:
3	chr2:171786011..171788954-chr2:172272838..172276305,3	K562	blood:
4	chr2:171787073..171789315-chr2:171814638..171817447,2	K562	blood:
5	chr2:171786521..171789315-chr2:171814811..171817447,2	K562	blood:
6	chr2:171786681..171789668-chr2:172749612..172751986,2	K562	blood:
7	chr2:171786011..171788954-chr2:172274093..172276305,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10515934	0.94[ASN][1000 genomes]
rs10803854	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10930448	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10930449	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11686985	0.82[EUR][1000 genomes]
rs11902360	0.84[EUR][1000 genomes]
rs11902369	0.86[EUR][1000 genomes]
rs12151587	0.81[ASN][1000 genomes]
rs12471930	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12612871	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12621769	0.82[EUR][1000 genomes]
rs12988738	0.83[ASN][1000 genomes]
rs12996518	0.94[ASN][1000 genomes]
rs13000898	0.86[ASN][1000 genomes]
rs13011011	0.82[ASN][1000 genomes]
rs13015226	1.00[ASN][1000 genomes]
rs13025033	0.82[EUR][1000 genomes]
rs13026662	0.88[ASN][1000 genomes]
rs13035460	1.00[ASN][1000 genomes]
rs1529391	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16859050	0.84[EUR][1000 genomes]
rs16859066	0.94[ASN][1000 genomes]
rs16859081	0.85[ASN][1000 genomes]
rs17281735	0.94[ASN][1000 genomes]
rs2098999	0.83[EUR][1000 genomes]
rs2114738	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2195116	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2557799	0.88[ASN][1000 genomes]
rs34004615	0.85[ASN][1000 genomes]
rs34017170	0.85[ASN][1000 genomes]
rs34330182	0.82[ASN][1000 genomes]
rs34342928	0.91[ASN][1000 genomes]
rs34532258	0.88[ASN][1000 genomes]
rs34911788	1.00[ASN][1000 genomes]
rs35123411	0.94[ASN][1000 genomes]
rs35230775	0.88[ASN][1000 genomes]
rs35864840	0.85[ASN][1000 genomes]
rs35890547	0.94[ASN][1000 genomes]
rs35987434	0.88[ASN][1000 genomes]
rs3755124	0.84[EUR][1000 genomes]
rs3755125	1.00[ASN][1000 genomes]
rs3755126	0.83[EUR][1000 genomes]
rs3770435	0.80[ASN][1000 genomes]
rs3770438	0.89[EUR][1000 genomes]
rs3770440	0.94[ASN][1000 genomes]
rs3770441	1.00[ASN][1000 genomes]
rs3770442	0.88[ASN][1000 genomes]
rs3821090	0.82[ASN][1000 genomes]
rs4667667	0.83[EUR][1000 genomes]
rs4668343	0.83[EUR][1000 genomes]
rs4668344	0.83[EUR][1000 genomes]
rs4668345	0.83[EUR][1000 genomes]
rs4668346	0.83[EUR][1000 genomes]
rs4668349	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4668350	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4668354	0.87[EUR][1000 genomes]
rs4668355	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433266	0.83[EUR][1000 genomes]
rs6433267	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709077	0.85[ASN][1000 genomes]
rs6714164	0.88[ASN][1000 genomes]
rs6714300	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715386	1.00[ASN][1000 genomes]
rs6724493	1.00[ASN][1000 genomes]
rs6729847	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731774	0.84[EUR][1000 genomes]
rs6734903	0.85[ASN][1000 genomes]
rs6742564	0.83[EUR][1000 genomes]
rs6742797	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6743201	0.85[ASN][1000 genomes]
rs71415229	1.00[ASN][1000 genomes]
rs71415231	0.82[ASN][1000 genomes]
rs71415232	0.94[ASN][1000 genomes]
rs71415233	0.82[ASN][1000 genomes]
rs731692	0.82[ASN][1000 genomes]
rs731693	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73976229	0.94[ASN][1000 genomes]
rs7559136	0.82[EUR][1000 genomes]
rs7567927	0.83[EUR][1000 genomes]
rs7570701	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7585607	0.83[EUR][1000 genomes]
rs960222	0.81[ASN][1000 genomes]
rs965518	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10803853	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171787000-171793800	Weak transcription	Gastric	stomach
2	chr2:171787000-171810400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:171787200-171790800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:171787200-171791000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:171787200-171791400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:171787200-171793200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:171787200-171793800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:171787200-171795200	Weak transcription	Ovary	ovary
9	chr2:171787400-171788600	Weak transcription	Left Ventricle	heart
10	chr2:171787400-171788800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:171787400-171789000	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr2:171787400-171789000	Enhancers	Rectal Smooth Muscle	rectum
13	chr2:171787400-171789400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr2:171787400-171790200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:171787400-171790600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:171787400-171790800	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:171787400-171790800	Weak transcription	Pancreas	Pancrea
18	chr2:171787400-171791000	Weak transcription	Lung	lung
19	chr2:171787400-171791200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr2:171787400-171791400	Weak transcription	Thymus	Thymus
21	chr2:171787400-171792200	Weak transcription	Fetal Thymus	thymus
22	chr2:171787400-171792800	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:171787400-171792800	Weak transcription	Spleen	Spleen
24	chr2:171787400-171793000	Weak transcription	Placenta	Placenta
25	chr2:171787400-171806000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:171787400-171806000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:171787400-171806000	Weak transcription	Esophagus	oesophagus
28	chr2:171787400-171806000	Weak transcription	Psoas Muscle	Psoas
29	chr2:171787400-171807200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:171787400-171808200	Weak transcription	Aorta	Aorta
31	chr2:171787400-171810000	Weak transcription	Small Intestine	intestine
32	chr2:171787600-171788600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:171787600-171789000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr2:171787600-171789000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr2:171787600-171789000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:171787600-171789000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:171787600-171789200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:171787600-171789200	Flanking Active TSS	HepG2	liver
39	chr2:171787600-171790200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr2:171787600-171790600	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr2:171787600-171790600	Enhancers	Liver	Liver
42	chr2:171787600-171791000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:171787600-171791000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:171787600-171793200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:171787600-171793800	Weak transcription	Right Ventricle	heart
46	chr2:171787600-171796600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:171787600-171806800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:171787600-171807600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:171787600-171829800	Weak transcription	Right Atrium	heart
50	chr2:171787800-171788600	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links