Variant report

Variant	rs1901545
Chromosome Location	chr3:85214203-85214204
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11127881	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12489229	0.80[YRI][hapmap]
rs1376937	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs17022359	0.89[AMR][1000 genomes]
rs17022521	1.00[AMR][1000 genomes]
rs17022531	0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022571	0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs17022605	0.85[YRI][hapmap]
rs17022612	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs17022614	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs17022646	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs17022655	0.82[YRI][hapmap]
rs17022680	0.81[YRI][hapmap]
rs17022682	0.81[YRI][hapmap]
rs17022685	0.85[YRI][hapmap]
rs2101343	0.81[AMR][1000 genomes]
rs2167605	0.82[YRI][hapmap];0.90[AMR][1000 genomes]
rs28658170	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28706252	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41495948	0.90[AMR][1000 genomes]
rs56701506	0.81[AMR][1000 genomes]
rs56773060	0.82[AFR][1000 genomes]
rs56792196	0.82[AFR][1000 genomes]
rs57628546	1.00[AMR][1000 genomes]
rs58051057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58222692	1.00[AMR][1000 genomes]
rs59333278	0.83[AFR][1000 genomes]
rs59636199	0.83[AFR][1000 genomes]
rs59867516	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59905205	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60149715	0.83[AFR][1000 genomes]
rs60184399	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60222151	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60319509	1.00[AMR][1000 genomes]
rs60958536	0.83[AFR][1000 genomes]
rs61212713	0.90[AMR][1000 genomes]
rs61290738	0.83[AFR][1000 genomes]
rs61484584	0.83[AFR][1000 genomes]
rs6770568	0.81[AMR][1000 genomes]
rs6783617	0.86[YRI][hapmap];0.81[AMR][1000 genomes]
rs6791040	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs6793583	0.81[AMR][1000 genomes]
rs6809971	0.81[AMR][1000 genomes]
rs72903386	0.90[AMR][1000 genomes]
rs72905240	0.90[AMR][1000 genomes]
rs72905270	0.81[AMR][1000 genomes]
rs72905294	1.00[AMR][1000 genomes]
rs72905295	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907103	1.00[AMR][1000 genomes]
rs72907149	1.00[AMR][1000 genomes]
rs72907158	1.00[AMR][1000 genomes]
rs72907161	1.00[AMR][1000 genomes]
rs72907167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907169	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907192	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72909170	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72909172	0.90[AMR][1000 genomes]
rs72909174	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72909176	0.90[AMR][1000 genomes]
rs72913051	0.84[AFR][1000 genomes]
rs72915062	0.83[AFR][1000 genomes]
rs72915065	0.83[AFR][1000 genomes]
rs72915067	0.82[AFR][1000 genomes]
rs72915102	0.81[AFR][1000 genomes]
rs72917112	0.81[AFR][1000 genomes]
rs72917132	0.81[AFR][1000 genomes]
rs72917137	0.81[AFR][1000 genomes]
rs72917150	0.81[AFR][1000 genomes]
rs72917154	0.81[AFR][1000 genomes]
rs72917160	0.81[AFR][1000 genomes]
rs72917162	0.81[AFR][1000 genomes]
rs72917164	0.81[AFR][1000 genomes]
rs72919227	0.83[AFR][1000 genomes]
rs7614097	1.00[AMR][1000 genomes]
rs7618389	0.88[YRI][hapmap]
rs7632253	0.90[AMR][1000 genomes]
rs7643603	1.00[AMR][1000 genomes]
rs7644008	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs7648045	0.83[AFR][1000 genomes]
rs9917693	0.89[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3419993	chr3:85030343-85663403	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
3	nsv492289	chr3:85066623-85319147	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2753915	chr3:85071410-85624810	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
5	nsv877094	chr3:85124697-85253981	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv590898	chr3:85158733-85243777	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv877095	chr3:85163167-85290434	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv877096	chr3:85163167-85366517	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv460747	chr3:85163167-85391672	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv590899	chr3:85163167-85391672	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1001124	chr3:85167047-85309046	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv590900	chr3:85177049-85265011	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv877097	chr3:85177173-85290434	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv877098	chr3:85177173-85361645	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv460748	chr3:85194054-85302473	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv460749	chr3:85194054-85302473	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv590901	chr3:85194054-85302473	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv470716	chr3:85194054-85316648	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv877099	chr3:85200179-85304062	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv590902	chr3:85200742-85302473	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv590903	chr3:85200742-85316648	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85212600-85214400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:85214000-85220600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:85214200-85225600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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