Variant report

Variant	rs1228183
Chromosome Location	chr3:100037644-100037645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100035534..100037682-chr3:100119496..100121597,2	MCF-7	breast:
2	chr3:100036672..100038736-chr3:100043578..100046026,2	K562	blood:
3	chr3:100035459..100037890-chr3:100081893..100083767,2	MCF-7	breast:
4	chr3:100036136..100038823-chr3:100040287..100043748,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10511178	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10936147	0.84[EUR][1000 genomes]
rs11709240	0.81[EUR][1000 genomes]
rs11709563	0.83[EUR][1000 genomes]
rs11710065	0.84[EUR][1000 genomes]
rs12629226	0.84[EUR][1000 genomes]
rs12633745	0.81[EUR][1000 genomes]
rs13072367	0.84[EUR][1000 genomes]
rs13074365	0.80[EUR][1000 genomes]
rs13075241	0.81[EUR][1000 genomes]
rs13078920	0.81[EUR][1000 genomes]
rs13079423	0.83[EUR][1000 genomes]
rs13079881	0.81[EUR][1000 genomes]
rs13098188	0.84[EUR][1000 genomes]
rs16842060	0.81[EUR][1000 genomes]
rs16847139	0.84[EUR][1000 genomes]
rs1979540	0.81[EUR][1000 genomes]
rs2129202	0.97[ASN][1000 genomes]
rs2289509	0.84[EUR][1000 genomes]
rs34314126	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34384409	0.84[EUR][1000 genomes]
rs34700788	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34869521	0.81[EUR][1000 genomes]
rs35141973	0.81[EUR][1000 genomes]
rs35594119	0.81[EUR][1000 genomes]
rs3772694	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3772696	0.81[EUR][1000 genomes]
rs3772697	0.83[EUR][1000 genomes]
rs3772701	0.81[EUR][1000 genomes]
rs3806616	0.81[EUR][1000 genomes]
rs4263320	0.84[EUR][1000 genomes]
rs4928115	0.81[EUR][1000 genomes]
rs4928121	0.81[EUR][1000 genomes]
rs4928122	0.81[EUR][1000 genomes]
rs4928163	0.81[EUR][1000 genomes]
rs4928165	0.84[EUR][1000 genomes]
rs4928168	0.84[EUR][1000 genomes]
rs59233020	0.81[EUR][1000 genomes]
rs61095099	0.81[EUR][1000 genomes]
rs66757043	0.81[EUR][1000 genomes]
rs67403774	0.81[EUR][1000 genomes]
rs6762794	0.85[EUR][1000 genomes]
rs6763680	0.84[EUR][1000 genomes]
rs6764125	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6764957	0.81[EUR][1000 genomes]
rs6765158	0.81[EUR][1000 genomes]
rs6772774	0.84[EUR][1000 genomes]
rs6774538	0.84[EUR][1000 genomes]
rs6787142	0.84[EUR][1000 genomes]
rs6787301	0.86[EUR][1000 genomes]
rs6791887	0.83[EUR][1000 genomes]
rs6794668	0.81[EUR][1000 genomes]
rs6800780	0.97[ASN][1000 genomes]
rs6808469	0.84[EUR][1000 genomes]
rs68094410	0.81[EUR][1000 genomes]
rs71313591	0.86[EUR][1000 genomes]
rs7611566	0.81[EUR][1000 genomes]
rs7615300	0.81[EUR][1000 genomes]
rs7625101	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1228183	TBC1D23	cis	Muscle Skeletal	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100053200	Weak transcription	Gastric	stomach
2	chr3:99994400-100040800	Weak transcription	Esophagus	oesophagus
3	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
5	chr3:100007000-100045000	Weak transcription	Lung	lung
6	chr3:100008600-100053000	Weak transcription	Aorta	Aorta
7	chr3:100009200-100045000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:100014600-100042200	Weak transcription	Fetal Brain Male	brain
9	chr3:100015400-100053200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:100019000-100043200	Weak transcription	Brain Angular Gyrus	brain
11	chr3:100019200-100038200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:100019600-100053000	Weak transcription	Colonic Mucosa	Colon
13	chr3:100020000-100038600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:100020600-100053000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:100020600-100053000	Weak transcription	Hela-S3	cervix
16	chr3:100021800-100052800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:100021800-100053000	Weak transcription	Psoas Muscle	Psoas
18	chr3:100022000-100047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:100022000-100052800	Weak transcription	Pancreas	Pancrea
20	chr3:100025800-100038800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:100025800-100053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:100025800-100053000	Weak transcription	Right Ventricle	heart
23	chr3:100026000-100038600	Weak transcription	HMEC	breast
24	chr3:100026000-100052600	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:100026000-100052800	Weak transcription	Thymus	Thymus
26	chr3:100026200-100038600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:100026400-100038400	Weak transcription	Ovary	ovary
28	chr3:100026400-100038600	Weak transcription	Brain Germinal Matrix	brain
29	chr3:100026400-100038600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:100026400-100038800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:100026400-100038800	Weak transcription	K562	blood
32	chr3:100026400-100045600	Weak transcription	HSMMtube	muscle
33	chr3:100026400-100052800	Weak transcription	NHEK	skin
34	chr3:100026400-100053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:100026600-100048600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr3:100026600-100052800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:100029200-100038200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:100029200-100038400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:100029400-100038400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:100029400-100038600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr3:100029400-100041200	Weak transcription	Fetal Kidney	kidney
42	chr3:100029600-100053000	Weak transcription	Brain Substantia Nigra	brain
43	chr3:100029800-100038600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:100029800-100038600	Weak transcription	Brain Anterior Caudate	brain
45	chr3:100029800-100039800	Weak transcription	Fetal Lung	lung
46	chr3:100030200-100038400	Weak transcription	HepG2	liver
47	chr3:100030200-100049800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:100030200-100053000	Weak transcription	Fetal Brain Female	brain
49	chr3:100030400-100038200	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:100030800-100038600	Weak transcription	Primary B cells from cord blood	blood

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