Variant report

Variant	rs581950
Chromosome Location	chr18:39603810-39603811
allele	C/T
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	NFIC	chr18:39603806-39604527	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
PIK3C3	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10221315	0.94[CEU][hapmap];0.87[CHB][hapmap]
rs10468957	0.80[EUR][1000 genomes]
rs10775471	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11082255	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11082257	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12455038	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12455083	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12455780	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12456084	0.86[EUR][1000 genomes]
rs12456573	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12456761	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12456934	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12457082	0.81[EUR][1000 genomes]
rs12457086	0.81[EUR][1000 genomes]
rs12457354	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12457525	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12964834	0.86[EUR][1000 genomes]
rs12964931	0.80[EUR][1000 genomes]
rs12966303	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13381503	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1368025	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1432138	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1557418	0.80[EUR][1000 genomes]
rs16975431	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16975474	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1897396	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1897397	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1941526	0.86[EUR][1000 genomes]
rs1941532	0.81[EUR][1000 genomes]
rs1942151	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1942152	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1984366	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1984367	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2043220	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2156015	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2334943	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34966612	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4890221	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4890377	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4890378	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4890379	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5004531	0.86[EUR][1000 genomes]
rs510946	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs569983	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57794431	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60861018	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61107251	0.86[EUR][1000 genomes]
rs62082282	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62082880	0.86[EUR][1000 genomes]
rs627099	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs639660	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs650586	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6507451	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs657164	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs667503	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs66960332	0.86[EUR][1000 genomes]
rs7237459	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7239288	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7241193	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7504589	0.84[EUR][1000 genomes]
rs8093251	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9304263	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9807114	0.80[EUR][1000 genomes]
rs9807279	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9807400	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9807487	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9948913	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9989595	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066869	chr18:38742896-39680723	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv543685	chr18:38742896-39680723	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv431979	chr18:39255558-39696452	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1066029	chr18:39322920-39623625	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv543686	chr18:39322920-39623625	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv909566	chr18:39327962-39688452	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
8	esv34153	chr18:39398768-39872265	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv909567	chr18:39470190-39652939	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
10	nsv909568	chr18:39491873-39768746	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39536000-39621800	Weak transcription	Stomach Mucosa	stomach
2	chr18:39536800-39633600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr18:39548400-39670000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr18:39564600-39606400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr18:39572000-39654400	Weak transcription	Colonic Mucosa	Colon
6	chr18:39577400-39610000	Weak transcription	Fetal Brain Male	brain
7	chr18:39578400-39663200	Weak transcription	Fetal Heart	heart
8	chr18:39581000-39604000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr18:39581000-39609200	Weak transcription	Fetal Intestine Small	intestine
10	chr18:39581000-39610200	Weak transcription	Aorta	Aorta
11	chr18:39581000-39647400	Weak transcription	Spleen	Spleen
12	chr18:39581000-39666200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr18:39582200-39605200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr18:39584600-39618600	Weak transcription	NHLF	lung
15	chr18:39585000-39611400	Weak transcription	Gastric	stomach
16	chr18:39585000-39646000	Weak transcription	Pancreas	Pancrea
17	chr18:39585000-39658600	Weak transcription	Small Intestine	intestine
18	chr18:39585200-39610400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr18:39585200-39612000	Weak transcription	NHEK	skin
20	chr18:39585400-39627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr18:39585600-39610200	Weak transcription	Brain Angular Gyrus	brain
22	chr18:39585600-39622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr18:39586000-39610200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr18:39586200-39605200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr18:39586400-39613000	Weak transcription	Brain Substantia Nigra	brain
26	chr18:39586400-39619000	Weak transcription	HUVEC	blood vessel
27	chr18:39586600-39610400	Weak transcription	Right Ventricle	heart
28	chr18:39586600-39647400	Weak transcription	Thymus	Thymus
29	chr18:39587000-39619400	Weak transcription	Lung	lung
30	chr18:39587200-39610600	Weak transcription	Fetal Stomach	stomach
31	chr18:39587200-39611400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr18:39587200-39614200	Weak transcription	Ovary	ovary
33	chr18:39589800-39606400	Strong transcription	HSMM	muscle
34	chr18:39590600-39668000	Weak transcription	Esophagus	oesophagus
35	chr18:39590800-39604000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr18:39590800-39607800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr18:39591800-39609800	Weak transcription	Brain Anterior Caudate	brain
38	chr18:39591800-39610800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr18:39592200-39629400	Weak transcription	Fetal Brain Female	brain
40	chr18:39594000-39609200	Weak transcription	Hela-S3	cervix
41	chr18:39594000-39614400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr18:39594600-39638800	Weak transcription	K562	blood
43	chr18:39595400-39605400	Weak transcription	Colon Smooth Muscle	Colon
44	chr18:39595400-39608400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr18:39595800-39605200	Weak transcription	HepG2	liver
46	chr18:39596000-39609800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr18:39596200-39618800	Weak transcription	Brain Germinal Matrix	brain
48	chr18:39596800-39605200	Weak transcription	Fetal Lung	lung
49	chr18:39597000-39610400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr18:39597200-39609800	Weak transcription	HMEC	breast

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