Variant report

Variant	rs3844041
Chromosome Location	chr1:57868316-57868317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10047071	0.85[CHD][hapmap]
rs10047073	0.85[CHD][hapmap]
rs10493219	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs10493221	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1077424	0.81[CHD][hapmap]
rs10889038	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs10889039	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs10889041	0.88[CHB][hapmap]
rs10889042	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889043	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889044	0.84[CHB][hapmap];0.93[ASN][1000 genomes]
rs11207007	0.88[CHB][hapmap];0.84[TSI][hapmap]
rs11207011	0.81[CHD][hapmap]
rs11207016	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs11207022	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11207024	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207025	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207026	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207027	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11207028	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207029	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585751	0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[ASN][1000 genomes]
rs11590708	0.88[CHB][hapmap]
rs11799925	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs11803514	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12087888	0.81[CHD][hapmap]
rs12092706	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119210	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs12126723	0.88[CHB][hapmap]
rs12136107	0.86[CHB][hapmap]
rs12137169	0.86[CHB][hapmap];0.88[CHD][hapmap];0.93[ASN][1000 genomes]
rs12139429	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs12240237	0.88[CHB][hapmap]
rs12565446	0.88[CHB][hapmap]
rs1424462	0.88[CHB][hapmap]
rs1424463	0.88[CHB][hapmap]
rs1424464	0.88[CHB][hapmap]
rs1424465	0.85[CHD][hapmap]
rs1424466	0.88[CHB][hapmap]
rs1424467	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs1424469	0.88[CHB][hapmap]
rs17115686	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs17115750	1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17423255	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs17424216	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs17425017	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs17456661	0.81[CHD][hapmap]
rs17458730	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17458751	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17459384	0.86[CHB][hapmap];0.93[ASN][1000 genomes]
rs1778032	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1778033	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1834151	0.88[CHB][hapmap]
rs1862925	0.85[CHD][hapmap]
rs2113454	0.81[ASN][1000 genomes]
rs2216808	0.85[CHD][hapmap]
rs2405697	0.85[CHD][hapmap]
rs2405994	0.86[CHB][hapmap];0.92[CHD][hapmap];0.93[ASN][1000 genomes]
rs267650	0.81[CHD][hapmap]
rs267651	0.85[CHD][hapmap]
rs269038	0.85[CHD][hapmap]
rs269042	0.90[JPT][hapmap]
rs269044	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs269045	0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs269048	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269049	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269050	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269051	0.82[ASN][1000 genomes]
rs269054	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs269057	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738553	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3850549	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3850550	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3850552	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3850556	0.83[ASW][hapmap];0.96[CEU][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3861834	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3896279	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3909556	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs3909557	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4912244	0.84[CHB][hapmap]
rs4912246	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4912247	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs511115	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515148	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516918	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs517825	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532926	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs539310	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs540431	0.81[CHD][hapmap];0.89[ASN][1000 genomes]
rs553674	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs563099	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563270	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564880	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs564951	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs565032	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs566847	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs567773	0.85[CHD][hapmap];0.83[MEX][hapmap]
rs61769670	0.81[ASN][1000 genomes]
rs61769756	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587767	0.85[CHD][hapmap]
rs6587768	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687842	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs6687934	0.84[CHD][hapmap]
rs72674892	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7528735	0.86[CHB][hapmap]
rs7535763	0.85[CHD][hapmap]
rs90940	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57858000-57868600	Weak transcription	Fetal Brain Male	brain
2	chr1:57860400-57874600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:57862400-57870800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:57862400-57873200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:57863800-57875400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr1:57864400-57873400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:57866600-57870600	Weak transcription	Stomach Mucosa	stomach
8	chr1:57867400-57872800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:57867600-57874400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:57867800-57870400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:57867800-57874600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:57867800-57875400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:57868000-57873600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:57868200-57870000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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