Variant report

Variant	rs10399821
Chromosome Location	chr1:225212719-225212720
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10399941	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10495231	0.90[ASN][1000 genomes]
rs10799293	0.83[ASN][1000 genomes]
rs10915744	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10915747	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs10915748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs10915749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10915750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10915751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10915757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10915758	0.83[ASN][1000 genomes]
rs10915761	0.90[ASN][1000 genomes]
rs10915762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10915763	0.90[ASN][1000 genomes]
rs10915778	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs10915780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10915781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10915785	0.83[ASN][1000 genomes]
rs10915788	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10915789	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11487462	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12059834	0.83[ASN][1000 genomes]
rs12061133	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12061172	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12061265	0.83[ASN][1000 genomes]
rs12062457	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12062461	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12066443	0.83[ASN][1000 genomes]
rs12067756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12068731	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12068939	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12069537	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12069808	0.83[ASN][1000 genomes]
rs12071270	0.83[ASN][1000 genomes]
rs12071453	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12071776	0.83[ASN][1000 genomes]
rs12072713	0.83[ASN][1000 genomes]
rs12073050	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12073648	0.83[ASN][1000 genomes]
rs12074130	0.83[ASN][1000 genomes]
rs12074382	0.83[ASN][1000 genomes]
rs12075769	0.83[ASN][1000 genomes]
rs12078470	0.83[ASN][1000 genomes]
rs12078559	0.83[ASN][1000 genomes]
rs12080062	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12082397	0.83[ASN][1000 genomes]
rs12084177	0.83[ASN][1000 genomes]
rs12084937	0.83[ASN][1000 genomes]
rs12086122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12086373	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12086473	0.83[ASN][1000 genomes]
rs12087715	0.83[ASN][1000 genomes]
rs12088836	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12092671	0.83[ASN][1000 genomes]
rs12093086	0.83[ASN][1000 genomes]
rs12093545	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs12095812	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12095892	0.83[ASN][1000 genomes]
rs12096616	0.83[ASN][1000 genomes]
rs1480102	0.83[ASN][1000 genomes]
rs1482278	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16844321	0.83[ASN][1000 genomes]
rs16844341	0.83[ASN][1000 genomes]
rs16844389	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16858965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2127558	0.83[ASN][1000 genomes]
rs2153246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2170110	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2449279	0.90[ASN][1000 genomes]
rs2449305	0.90[ASN][1000 genomes]
rs2449306	0.90[ASN][1000 genomes]
rs2456344	0.90[ASN][1000 genomes]
rs2456350	0.90[ASN][1000 genomes]
rs2456354	0.90[ASN][1000 genomes]
rs2501103	0.90[ASN][1000 genomes]
rs2501112	0.83[ASN][1000 genomes]
rs28793649	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs28871966	0.83[ASN][1000 genomes]
rs4275419	0.83[ASN][1000 genomes]
rs55708629	0.90[ASN][1000 genomes]
rs56302122	0.90[ASN][1000 genomes]
rs57262741	0.83[ASN][1000 genomes]
rs59730777	0.83[ASN][1000 genomes]
rs60782238	0.83[ASN][1000 genomes]
rs61483735	0.83[ASN][1000 genomes]
rs6656178	0.83[ASN][1000 genomes]
rs6662177	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6666025	0.83[ASN][1000 genomes]
rs6680233	0.90[ASN][1000 genomes]
rs6680659	0.83[ASN][1000 genomes]
rs6683197	0.83[ASN][1000 genomes]
rs6689287	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6689608	0.83[ASN][1000 genomes]
rs6698942	0.83[ASN][1000 genomes]
rs6700281	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6704159	0.83[ASN][1000 genomes]
rs74146611	0.90[ASN][1000 genomes]
rs74147131	0.83[ASN][1000 genomes]
rs74149426	0.83[ASN][1000 genomes]
rs74149428	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs74149436	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7418261	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7527885	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7533311	0.83[ASN][1000 genomes]
rs7535962	0.83[ASN][1000 genomes]
rs7550540	0.83[ASN][1000 genomes]
rs769297	0.83[ASN][1000 genomes]
rs9725252	0.83[ASN][1000 genomes]
rs9919164	0.86[AFR][1000 genomes];0.83[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:4 , 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

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