Variant report

Variant	rs2153929
Chromosome Location	chr1:72658214-72658215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1026566	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs1026567	1.00[JPT][hapmap]
rs10493493	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap]
rs10493494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11209923	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11209928	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11209932	0.88[ASN][1000 genomes]
rs11209933	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11209935	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11209938	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11583451	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11587829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11587895	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs1194265	0.82[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1194267	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1194269	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1194270	1.00[JPT][hapmap]
rs1194271	0.84[ASN][1000 genomes]
rs1194273	0.84[ASN][1000 genomes]
rs1194277	0.84[ASN][1000 genomes]
rs1194278	0.82[ASN][1000 genomes]
rs1194281	0.80[ASN][1000 genomes]
rs1194282	0.84[ASN][1000 genomes]
rs1194283	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1194284	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1194286	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12036585	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1205484	0.84[ASN][1000 genomes]
rs1209251	0.84[ASN][1000 genomes]
rs12117225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12124902	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12125336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12126162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12136617	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12137663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12139652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12141242	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1342863	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1342874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1385920	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1385921	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1486097	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1486111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1675356	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17524209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17525406	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17588282	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs17589316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1858600	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2066416	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2126077	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2298151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298152	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2422136	0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2630431	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2797540	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2797543	0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2821285	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2821288	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2821293	1.00[JPT][hapmap]
rs2821295	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs2821296	0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs55777234	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56062633	0.80[ASN][1000 genomes]
rs56248439	0.80[ASN][1000 genomes]
rs6656980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6659016	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668604	0.88[ASN][1000 genomes]
rs6698979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6699731	0.84[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6699841	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7349073	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7517387	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7518919	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7529364	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7549778	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs985227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1007073	chr1:72419858-72734657	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1006076	chr1:72477436-72700903	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv534996	chr1:72477436-72700903	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv428454	chr1:72504469-72926256	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv461906	chr1:72549836-72683226	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	nsv461917	chr1:72549836-72683226	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
8	nsv546480	chr1:72549836-72683226	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
9	nsv461928	chr1:72555489-72683226	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
10	nsv546481	chr1:72555489-72683226	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
11	nsv461939	chr1:72555489-72717743	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv546482	chr1:72555489-72717743	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv546483	chr1:72581966-72659880	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
14	nsv997768	chr1:72583375-72665268	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
15	nsv546484	chr1:72595125-72667196	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
16	nsv1013250	chr1:72603540-72762582	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv528210	chr1:72606418-72659880	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
18	nsv470715	chr1:72606418-72659880	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
19	nsv830192	chr1:72616562-72806118	Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv1000451	chr1:72618756-72658214	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
21	nsv461951	chr1:72634912-72707226	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
22	nsv546485	chr1:72634912-72707226	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
23	nsv1014832	chr1:72642420-72823477	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	nsv534997	chr1:72642420-72823477	Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
25	nsv546486	chr1:72654730-72729142	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2153929	NEGR1	cis	cerebellum	SCAN
rs2153929	RPE65	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72644400-72668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr1:72651400-72660200	Weak transcription	Osteobl	bone
3	chr1:72655000-72660000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:72655200-72663400	Weak transcription	NHDF-Ad	bronchial
5	chr1:72655400-72660200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr1:72655400-72663200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:72655400-72663400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:72655600-72658400	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:72657800-72658400	Enhancers	Rectal Smooth Muscle	rectum
10	chr1:72657800-72658400	Enhancers	Stomach Smooth Muscle	stomach
11	chr1:72657800-72659000	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr1:72658000-72660400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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