Variant report

Variant	rs4912244
Chromosome Location	chr1:57852994-57852995
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 134 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10047071	1.00[JPT][hapmap]
rs10047073	1.00[JPT][hapmap]
rs10493219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10493221	0.88[CHB][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10493225	0.86[JPT][hapmap]
rs10889034	0.86[JPT][hapmap]
rs10889042	0.88[CHB][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10889043	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10889044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11207007	0.88[CHB][hapmap]
rs11207010	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs11207011	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs11207020	0.84[ASN][1000 genomes]
rs11207021	0.86[ASN][1000 genomes]
rs11207022	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11207024	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207025	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207026	0.88[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207027	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207028	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207029	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11579258	0.86[ASN][1000 genomes]
rs11581250	0.86[ASN][1000 genomes]
rs11585284	0.86[ASN][1000 genomes]
rs11585751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11586826	0.86[ASN][1000 genomes]
rs11590652	0.82[ASN][1000 genomes]
rs11799925	0.88[CHB][hapmap]
rs11803514	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12044912	0.86[JPT][hapmap]
rs12046102	0.86[JPT][hapmap]
rs12061812	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12087888	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs12092706	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12124445	0.86[ASN][1000 genomes]
rs12125219	0.86[ASN][1000 genomes]
rs12127603	0.86[ASN][1000 genomes]
rs12128305	0.86[JPT][hapmap]
rs12132685	0.86[JPT][hapmap]
rs12136107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12137169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12137540	0.81[ASN][1000 genomes]
rs12139429	0.88[CHB][hapmap]
rs12142821	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1240442	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12405761	1.00[JPT][hapmap]
rs12566690	0.84[ASN][1000 genomes]
rs12568449	0.85[JPT][hapmap]
rs12726704	1.00[JPT][hapmap]
rs12752978	0.86[JPT][hapmap]
rs1334239	0.86[JPT][hapmap]
rs1334240	0.86[JPT][hapmap]
rs1424463	0.85[JPT][hapmap]
rs166514	0.86[JPT][hapmap]
rs17115685	0.86[ASN][1000 genomes]
rs17115686	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17115750	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs17424216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17425017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17425189	0.86[JPT][hapmap]
rs17456661	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17457873	0.86[ASN][1000 genomes]
rs17458730	0.88[CHB][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17458751	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17459384	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17459948	0.86[JPT][hapmap]
rs1778032	0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778033	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2052615	0.82[ASN][1000 genomes]
rs2052616	0.82[ASN][1000 genomes]
rs2052617	0.86[ASN][1000 genomes]
rs2216808	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2405696	1.00[JPT][hapmap]
rs2405994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs267638	0.86[JPT][hapmap]
rs267647	0.86[JPT][hapmap]
rs267650	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs269044	0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs269048	0.88[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs269049	0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs269050	0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs269054	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs269057	0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2781325	0.86[JPT][hapmap]
rs3738553	0.88[CHB][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3844041	0.84[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3850549	0.88[CHB][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3850550	0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3850552	0.88[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3850556	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3861834	0.88[CHB][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3896279	0.88[CHB][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs390203	1.00[JPT][hapmap]
rs3909556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3909557	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4279875	0.86[JPT][hapmap]
rs439378	0.86[JPT][hapmap]
rs4912163	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4912246	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4912247	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs511115	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs515148	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs516918	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs517825	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs532926	0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539310	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs553674	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563099	0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs563270	0.88[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs564880	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564951	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs565032	0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs566847	0.88[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs567773	0.87[ASN][1000 genomes]
rs567916	0.86[ASN][1000 genomes]
rs61769756	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6587768	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6669975	1.00[JPT][hapmap]
rs6687842	0.88[CHB][hapmap]
rs72674892	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs736109	0.86[JPT][hapmap]
rs736110	0.86[JPT][hapmap]
rs746937	0.86[JPT][hapmap]
rs7513076	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7528735	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs7535763	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs7540817	0.84[ASN][1000 genomes]
rs9436130	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871943	chr1:57784144-57855876	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv871530	chr1:57793948-57858319	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv871968	chr1:57803349-57858319	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv954	chr1:57823140-57865799	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 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	chr1:57846600-57853400	Enhancers	Fetal Brain Male	brain
2	chr1:57848000-57859800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:57848200-57855000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:57851800-57855000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:57851800-57856200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:57851800-57857200	Weak transcription	Fetal Brain Female	brain

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