Variant report

Variant	rs28660667
Chromosome Location	chr2:40452902-40452903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10153786	0.87[AMR][1000 genomes]
rs10167744	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10167955	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175778	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176352	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176641	1.00[ASN][1000 genomes]
rs10183585	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199306	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202413	0.80[EUR][1000 genomes]
rs10207018	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207038	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10490207	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884718	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11884732	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885401	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887546	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887643	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889015	0.96[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890878	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891508	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891921	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894296	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11894882	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895025	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899204	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11903986	1.00[ASN][1000 genomes]
rs12329007	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006841	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13383126	1.00[ASN][1000 genomes]
rs13384452	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385280	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13389962	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398048	1.00[ASN][1000 genomes]
rs13398809	1.00[ASN][1000 genomes]
rs13400484	1.00[ASN][1000 genomes]
rs13403847	0.81[EUR][1000 genomes]
rs13408531	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13414508	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428581	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428681	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366424	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428574	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025234	1.00[ASN][1000 genomes]
rs17025260	1.00[ASN][1000 genomes]
rs17025271	1.00[ASN][1000 genomes]
rs17025453	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025510	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025570	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025628	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17038992	1.00[ASN][1000 genomes]
rs17570537	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1896712	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033230	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2041827	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28380530	1.00[ASN][1000 genomes]
rs374153	1.00[ASN][1000 genomes]
rs390579	1.00[ASN][1000 genomes]
rs400673	1.00[ASN][1000 genomes]
rs405416	1.00[ASN][1000 genomes]
rs423177	1.00[ASN][1000 genomes]
rs440387	1.00[ASN][1000 genomes]
rs56092525	0.81[EUR][1000 genomes]
rs6704907	1.00[ASN][1000 genomes]
rs6720270	1.00[ASN][1000 genomes]
rs6728644	1.00[ASN][1000 genomes]
rs6729089	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758015	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760003	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71439287	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924568	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924573	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73926129	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs73926130	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73927124	1.00[ASN][1000 genomes]
rs741320	1.00[ASN][1000 genomes]
rs7562916	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563045	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563290	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563445	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7567178	1.00[ASN][1000 genomes]
rs7570501	1.00[ASN][1000 genomes]
rs7570522	1.00[ASN][1000 genomes]
rs7575693	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575802	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583602	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589951	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601672	1.00[ASN][1000 genomes]
rs7601991	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602006	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602342	1.00[ASN][1000 genomes]
rs7602377	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605482	1.00[ASN][1000 genomes]
rs7607992	1.00[ASN][1000 genomes]
rs9309053	1.00[ASN][1000 genomes]
rs9653516	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv524586	chr2:40447587-40497501	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40437200-40453200	Weak transcription	Right Ventricle	heart
2	chr2:40446400-40454400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:40446400-40455400	Weak transcription	Psoas Muscle	Psoas
4	chr2:40447800-40453000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:40447800-40454400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:40447800-40457600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:40448000-40487400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr2:40448200-40453600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr2:40448200-40455400	Weak transcription	HSMM	muscle
10	chr2:40450400-40453600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:40451200-40454200	Weak transcription	Osteobl	bone
12	chr2:40451400-40455600	Weak transcription	Aorta	Aorta
13	chr2:40451400-40490000	Weak transcription	Dnd41	blood
14	chr2:40451600-40453600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:40451800-40453600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr2:40452000-40454600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:40452200-40453400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr2:40452200-40453600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:40452200-40453600	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr2:40452200-40453600	Enhancers	HSMMtube	muscle
21	chr2:40452200-40453800	Enhancers	Rectal Smooth Muscle	rectum
22	chr2:40452200-40454000	Enhancers	Fetal Brain Male	brain
23	chr2:40452200-40454000	Enhancers	Fetal Brain Female	brain
24	chr2:40452400-40453600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr2:40452400-40454400	Enhancers	Fetal Heart	heart
26	chr2:40452400-40454800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:40452600-40453600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:40452600-40453600	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr2:40452600-40453800	Enhancers	Fetal Muscle Leg	muscle
30	chr2:40452600-40453800	Enhancers	Fetal Stomach	stomach
31	chr2:40452600-40454200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:40452600-40454200	Enhancers	Stomach Smooth Muscle	stomach
33	chr2:40452600-40454600	Enhancers	Colon Smooth Muscle	Colon
34	chr2:40452600-40455600	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr2:40452800-40453400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr2:40452800-40453400	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr2:40452800-40453400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr2:40452800-40453400	Enhancers	Fetal Lung	lung
39	chr2:40452800-40453600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:40452800-40453600	Enhancers	Left Ventricle	heart
41	chr2:40452800-40454000	Enhancers	Brain Germinal Matrix	brain

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