Variant report

Variant	rs10399941
Chromosome Location	chr1:225215123-225215124
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225208646..225211614-chr1:225214288..225217124,2	K562	blood:

Extended variants
information (count: 191 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs10399821	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10495231	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10799282	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10799283	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10799293	0.92[ASN][1000 genomes]
rs10915733	0.81[ASN][1000 genomes]
rs10915743	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10915744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10915745	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10915747	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10915748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10915749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10915750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10915751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10915757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10915758	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10915761	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10915762	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10915763	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10915778	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10915780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10915781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10915785	0.92[ASN][1000 genomes]
rs10915786	0.89[ASN][1000 genomes]
rs10915788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10915789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10915795	0.89[ASN][1000 genomes]
rs10915799	0.89[ASN][1000 genomes]
rs10915800	0.89[ASN][1000 genomes]
rs10915801	0.89[ASN][1000 genomes]
rs11484699	0.89[ASN][1000 genomes]
rs11484714	0.89[ASN][1000 genomes]
rs11484715	0.89[ASN][1000 genomes]
rs11487461	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11487462	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11487470	0.89[ASN][1000 genomes]
rs12059834	0.92[ASN][1000 genomes]
rs12060676	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12061133	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12061172	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12061265	0.92[ASN][1000 genomes]
rs12061874	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12062457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12062461	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12064443	0.89[ASN][1000 genomes]
rs12064759	0.89[ASN][1000 genomes]
rs12066443	0.92[ASN][1000 genomes]
rs12066458	0.89[ASN][1000 genomes]
rs12067725	0.89[ASN][1000 genomes]
rs12067756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12068014	0.89[ASN][1000 genomes]
rs12068731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12068939	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12069353	0.89[ASN][1000 genomes]
rs12069461	0.89[ASN][1000 genomes]
rs12069537	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12069808	0.92[ASN][1000 genomes]
rs12070493	0.89[ASN][1000 genomes]
rs12071270	0.92[ASN][1000 genomes]
rs12071453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12071776	0.92[ASN][1000 genomes]
rs12072713	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12073050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12073648	0.92[ASN][1000 genomes]
rs12074130	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12074382	0.92[ASN][1000 genomes]
rs12074477	0.85[ASN][1000 genomes]
rs12074718	0.89[ASN][1000 genomes]
rs12075769	0.92[ASN][1000 genomes]
rs12077191	0.81[ASN][1000 genomes]
rs12078470	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12078559	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12078696	0.89[ASN][1000 genomes]
rs12079258	0.89[ASN][1000 genomes]
rs12080062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12081545	0.89[ASN][1000 genomes]
rs12082397	0.92[ASN][1000 genomes]
rs12084177	0.92[ASN][1000 genomes]
rs12084937	0.92[ASN][1000 genomes]
rs12085406	0.89[ASN][1000 genomes]
rs12086122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12086185	0.89[ASN][1000 genomes]
rs12086373	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12086473	0.92[ASN][1000 genomes]
rs12087715	0.92[ASN][1000 genomes]
rs12088357	0.89[ASN][1000 genomes]
rs12088836	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12089294	0.89[ASN][1000 genomes]
rs12089735	0.89[ASN][1000 genomes]
rs12090519	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12091019	0.89[ASN][1000 genomes]
rs12091058	0.89[ASN][1000 genomes]
rs12091059	0.89[ASN][1000 genomes]
rs12092293	0.89[ASN][1000 genomes]
rs12092671	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12093086	0.92[ASN][1000 genomes]
rs12093545	0.86[CHB][hapmap];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12094453	0.89[ASN][1000 genomes]
rs12094780	0.89[ASN][1000 genomes]
rs12095812	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12095841	0.85[ASN][1000 genomes]
rs12095892	0.92[ASN][1000 genomes]
rs12096616	0.92[ASN][1000 genomes]
rs12097555	0.89[ASN][1000 genomes]
rs1480102	0.92[ASN][1000 genomes]
rs1480108	0.89[ASN][1000 genomes]
rs1482278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1600530	0.89[ASN][1000 genomes]
rs16844321	0.92[ASN][1000 genomes]
rs16844341	0.92[ASN][1000 genomes]
rs16844389	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs16844455	0.89[ASN][1000 genomes]
rs16858094	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16858965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1842335	0.89[ASN][1000 genomes]
rs2127558	0.92[ASN][1000 genomes]
rs2153246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2170110	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2244108	0.85[ASN][1000 genomes]
rs2244109	0.85[ASN][1000 genomes]
rs2244198	0.85[ASN][1000 genomes]
rs2254430	0.85[ASN][1000 genomes]
rs2406099	0.85[ASN][1000 genomes]
rs2449279	1.00[ASN][1000 genomes]
rs2449305	1.00[ASN][1000 genomes]
rs2449306	1.00[ASN][1000 genomes]
rs2456344	1.00[ASN][1000 genomes]
rs2456350	1.00[ASN][1000 genomes]
rs2456354	1.00[ASN][1000 genomes]
rs2501103	1.00[ASN][1000 genomes]
rs2501112	0.92[ASN][1000 genomes]
rs2662910	0.85[ASN][1000 genomes]
rs2662911	0.85[ASN][1000 genomes]
rs2662913	0.85[ASN][1000 genomes]
rs2802546	0.85[ASN][1000 genomes]
rs2802567	0.85[ASN][1000 genomes]
rs2802736	0.85[ASN][1000 genomes]
rs28510743	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28673436	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28793649	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs28871966	0.92[ASN][1000 genomes]
rs3991375	0.89[ASN][1000 genomes]
rs4256778	0.85[ASN][1000 genomes]
rs4275419	0.92[ASN][1000 genomes]
rs55708629	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56302122	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57262741	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59318794	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59730777	0.92[ASN][1000 genomes]
rs60619295	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60782238	0.92[ASN][1000 genomes]
rs61483735	0.92[ASN][1000 genomes]
rs6656178	0.92[ASN][1000 genomes]
rs6662177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6666025	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6680233	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6680659	0.92[ASN][1000 genomes]
rs6683197	0.92[ASN][1000 genomes]
rs6689287	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6689608	0.92[ASN][1000 genomes]
rs6694400	0.85[ASN][1000 genomes]
rs6698942	0.92[ASN][1000 genomes]
rs6700281	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6704159	0.92[ASN][1000 genomes]
rs74146611	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74147131	0.92[ASN][1000 genomes]
rs74149417	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs74149420	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs74149426	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs74149428	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs74149429	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs74149436	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7418261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7527885	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7533311	0.92[ASN][1000 genomes]
rs7533616	0.85[ASN][1000 genomes]
rs7535962	0.92[ASN][1000 genomes]
rs7543666	0.89[ASN][1000 genomes]
rs7550540	0.92[ASN][1000 genomes]
rs769297	0.92[ASN][1000 genomes]
rs9725252	0.92[ASN][1000 genomes]
rs9919164	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9919334	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757773	chr1:225087924-225253274	Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv2759001	chr1:225087924-225253274	Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv3438976	chr1:225133567-225248753	Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv873225	chr1:225162060-225373936	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv549262	chr1:225191852-225319898	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv549263	chr1:225202426-225319898	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv1805842	chr1:225208247-225217265	Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv998899	chr1:225210813-225496353	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225204000-225217400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:225205600-225215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:225205600-225235600	Weak transcription	Pancreas	Pancrea
4	chr1:225211200-225226800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:225213000-225215200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:225214400-225216400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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