Variant report

Variant	rs13408945
Chromosome Location	chr2:33421307-33421308
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10048733	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10084248	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10167324	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167399	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170980	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173416	0.89[ASN][1000 genomes]
rs10188467	0.81[AFR][1000 genomes]
rs10189948	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195782	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201015	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201397	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201620	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10204479	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205515	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10514773	0.89[ASN][1000 genomes]
rs11675702	0.89[ASN][1000 genomes]
rs11686962	0.89[ASN][1000 genomes]
rs11691887	0.89[ASN][1000 genomes]
rs11692723	0.85[ASN][1000 genomes]
rs11886226	0.89[ASN][1000 genomes]
rs11886337	1.00[ASN][1000 genomes]
rs11898777	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328471	0.80[AFR][1000 genomes]
rs13387581	0.80[AFR][1000 genomes]
rs13392128	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13401618	0.85[AFR][1000 genomes]
rs13417478	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13417974	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13431080	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17012612	0.94[ASN][1000 genomes]
rs17012615	0.94[ASN][1000 genomes]
rs17012621	0.94[ASN][1000 genomes]
rs17012646	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17012655	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17012657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17012674	1.00[ASN][1000 genomes]
rs17012680	0.94[ASN][1000 genomes]
rs17012691	1.00[ASN][1000 genomes]
rs17012720	0.85[ASN][1000 genomes]
rs17012778	0.80[ASN][1000 genomes]
rs2004437	0.85[ASN][1000 genomes]
rs2290427	0.85[ASN][1000 genomes]
rs2290447	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4578839	0.94[ASN][1000 genomes]
rs4641915	0.94[ASN][1000 genomes]
rs55852365	0.85[ASN][1000 genomes]
rs57095191	1.00[ASN][1000 genomes]
rs57119251	1.00[ASN][1000 genomes]
rs57408328	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60523332	1.00[ASN][1000 genomes]
rs60912788	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61609498	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61754245	0.89[ASN][1000 genomes]
rs6543693	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6543694	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6543695	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6543696	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543697	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6706122	1.00[ASN][1000 genomes]
rs6718325	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6721333	0.84[AFR][1000 genomes]
rs6722904	0.89[ASN][1000 genomes]
rs6728561	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730109	0.94[ASN][1000 genomes]
rs6730341	0.94[ASN][1000 genomes]
rs6734291	1.00[ASN][1000 genomes]
rs6746796	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752708	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757287	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757381	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760864	0.89[ASN][1000 genomes]
rs72855723	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72855746	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72855774	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72855787	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72858006	0.80[AFR][1000 genomes]
rs72858037	1.00[ASN][1000 genomes]
rs72858071	0.89[ASN][1000 genomes]
rs72858072	0.89[ASN][1000 genomes]
rs73927364	0.85[ASN][1000 genomes]
rs7568506	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7583435	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7603774	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606937	1.00[ASN][1000 genomes]
rs9308932	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964701	1.00[ASN][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	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	esv33628	chr2:33257484-33455355	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv873790	chr2:33369582-33466483	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33403800-33489800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:33408000-33422400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:33408200-33423000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:33409200-33441600	Weak transcription	Psoas Muscle	Psoas
5	chr2:33410400-33423800	Weak transcription	Placenta	Placenta
6	chr2:33410400-33438000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:33412400-33421400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:33414000-33427800	Weak transcription	Right Ventricle	heart
9	chr2:33414000-33434200	Weak transcription	HUVEC	blood vessel
10	chr2:33414200-33422400	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:33414600-33422400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:33414600-33455400	Weak transcription	Fetal Stomach	stomach
13	chr2:33415000-33434400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:33415200-33427600	Weak transcription	Left Ventricle	heart
15	chr2:33415200-33441600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:33415400-33441600	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:33415600-33427000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr2:33415600-33431800	Weak transcription	NHDF-Ad	bronchial
19	chr2:33415600-33434200	Weak transcription	K562	blood
20	chr2:33415800-33431800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:33417000-33421800	Weak transcription	Fetal Heart	heart
22	chr2:33417400-33431800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:33418200-33422000	Weak transcription	Liver	Liver
24	chr2:33418200-33433400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:33418400-33435000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr2:33418800-33427000	Weak transcription	Ovary	ovary
27	chr2:33419000-33434200	Weak transcription	NH-A	brain
28	chr2:33419400-33427400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:33419800-33427800	Weak transcription	Aorta	Aorta
30	chr2:33420000-33432000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:33420600-33423000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:33420800-33430400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:33421000-33426800	Weak transcription	Osteobl	bone
34	chr2:33421000-33427400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:33421000-33427400	Weak transcription	NHLF	lung
36	chr2:33421200-33422600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:33421200-33427200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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