Variant report

Variant	rs12748679
Chromosome Location	chr1:72644585-72644586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10789334	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12725081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12726084	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755450	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1385919	0.87[GIH][hapmap];0.87[ASN][1000 genomes]
rs1545933	0.85[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs1858601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1905978	0.87[GIH][hapmap];0.88[MEX][hapmap];0.87[ASN][1000 genomes]
rs2821248	0.87[ASN][1000 genomes]
rs2901653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34029663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34124399	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34274959	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34289700	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34840702	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34940719	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35166058	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35483896	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35944729	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36075373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61765640	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6665041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9699942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 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	nsv1010315	chr1:72615648-72653421	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
20	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
21	nsv998410	chr1:72618544-72651819	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
22	nsv999081	chr1:72618544-72653421	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
23	nsv1009412	chr1:72618756-72651449	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	n/a	n/a	inside rSNPs	diseases
24	nsv1013666	chr1:72618756-72653421	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
25	nsv1000451	chr1:72618756-72658214	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
26	nsv516389	chr1:72621463-72657058	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
27	nsv461951	chr1:72634912-72707226	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
28	nsv546485	chr1:72634912-72707226	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	n/a	n/a	inside rSNPs	diseases
29	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
30	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72643400-72644800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr1:72643600-72644600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:72643600-72644600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:72643600-72645200	Enhancers	Rectal Smooth Muscle	rectum
5	chr1:72644200-72644600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:72644400-72644600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:72644400-72648800	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:72644400-72649000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:72644400-72649000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:72644400-72649200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:72644400-72649200	Weak transcription	Osteobl	bone
12	chr1:72644400-72668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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