Variant report

Variant	rs17424216
Chromosome Location	chr1:57845605-57845606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 163 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10047071	0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10047072	0.82[ASN][1000 genomes]
rs10047073	0.81[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10047177	0.83[ASN][1000 genomes]
rs10047179	0.80[ASN][1000 genomes]
rs10493219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493221	0.90[CHB][hapmap]
rs10493225	0.86[JPT][hapmap]
rs1077424	0.92[CHD][hapmap]
rs10889034	0.86[JPT][hapmap]
rs10889038	0.81[CHB][hapmap];0.96[CHD][hapmap]
rs10889039	0.81[CHB][hapmap];0.96[CHD][hapmap]
rs10889041	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs10889042	0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs10889044	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs11207007	0.81[CHB][hapmap]
rs11207010	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11207011	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs11207016	0.81[CHB][hapmap];0.96[CHD][hapmap]
rs11207020	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11207021	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207022	0.93[ASN][1000 genomes]
rs11207026	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs11207027	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11579258	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581250	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585284	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585751	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs11586826	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590652	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590708	0.81[CHB][hapmap]
rs11799925	0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs12044912	0.86[JPT][hapmap]
rs12046102	0.86[JPT][hapmap]
rs12061812	0.90[CHB][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs12067263	0.82[ASN][1000 genomes]
rs12087888	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs12119210	0.81[CHB][hapmap];0.96[CHD][hapmap]
rs12124445	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125219	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126723	0.81[CHB][hapmap]
rs12127603	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128305	0.86[JPT][hapmap]
rs12132685	0.86[JPT][hapmap]
rs12136107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137169	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs12137540	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12137583	0.83[ASN][1000 genomes]
rs12139429	0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs12142821	0.83[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12240237	0.81[CHB][hapmap]
rs1240442	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1240443	0.82[ASN][1000 genomes]
rs12405761	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12565446	0.81[CHB][hapmap]
rs12566690	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs1424464	0.81[CHB][hapmap]
rs1424465	0.96[CHD][hapmap]
rs1424466	0.81[CHB][hapmap]
rs1424467	0.81[CHB][hapmap];0.96[CHD][hapmap]
rs1424469	0.81[CHB][hapmap]
rs1557222	0.82[ASN][1000 genomes]
rs166514	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs17115685	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17115750	0.90[CHB][hapmap]
rs17423255	0.81[CHB][hapmap];0.96[CHD][hapmap]
rs17425017	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17425189	0.86[JPT][hapmap]
rs17456661	0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.83[ASN][1000 genomes]
rs17457873	0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17458730	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs17458751	0.84[ASN][1000 genomes]
rs17459384	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs17459948	0.86[JPT][hapmap]
rs1778032	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs1778033	0.84[ASN][1000 genomes]
rs1834151	0.81[CHB][hapmap]
rs1862925	0.96[CHD][hapmap]
rs2052615	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052616	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2052617	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2113453	0.80[ASN][1000 genomes]
rs2113454	0.82[ASN][1000 genomes]
rs2216808	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2405696	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2405697	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs2405994	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs267638	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs267647	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs267650	0.81[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs267651	0.96[CHD][hapmap]
rs269038	0.96[CHD][hapmap];0.82[ASN][1000 genomes]
rs269039	0.82[ASN][1000 genomes]
rs269044	0.90[CHB][hapmap]
rs269045	0.92[CHD][hapmap]
rs269048	0.90[CHB][hapmap]
rs269049	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs269050	0.90[CHB][hapmap]
rs269057	0.90[CHB][hapmap]
rs2781325	0.86[JPT][hapmap]
rs3738553	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs3844041	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs3850549	0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs3850550	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs3850552	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs3850556	0.92[CHD][hapmap]
rs3861833	0.82[ASN][1000 genomes]
rs3861834	0.90[CHB][hapmap];0.96[CHD][hapmap];0.84[ASN][1000 genomes]
rs3896279	0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs390203	1.00[JPT][hapmap]
rs3909556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3909557	0.93[ASN][1000 genomes]
rs3909558	0.82[ASN][1000 genomes]
rs4279875	0.86[JPT][hapmap]
rs439378	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4912162	0.83[ASN][1000 genomes]
rs4912163	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4912237	0.83[ASN][1000 genomes]
rs4912244	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4912246	0.84[ASN][1000 genomes]
rs532926	0.90[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs539310	0.84[ASN][1000 genomes]
rs540431	0.92[CHD][hapmap]
rs553674	0.84[ASN][1000 genomes]
rs55863020	0.83[ASN][1000 genomes]
rs563099	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs563270	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs564880	0.84[ASN][1000 genomes]
rs564951	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs565032	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs566847	0.90[CHB][hapmap];0.96[CHD][hapmap];0.84[ASN][1000 genomes]
rs567773	0.96[CHD][hapmap]
rs61769670	0.82[ASN][1000 genomes]
rs61769725	0.91[ASN][1000 genomes]
rs6587767	0.96[CHD][hapmap]
rs6669975	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6687842	0.90[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs6687934	0.96[CHD][hapmap]
rs6690017	0.89[ASN][1000 genomes]
rs72674872	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72674892	0.84[ASN][1000 genomes]
rs736109	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs736110	0.86[JPT][hapmap]
rs746937	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs7513076	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7528735	1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535763	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7540817	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs90940	0.92[CHD][hapmap]
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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17424216	DAB1	cis	cerebellum	SCAN
rs17424216	DIO1	cis	parietal	SCAN
rs17424216	PARS2	cis	cerebellum	SCAN
rs17424216	ITPKB	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57837400-57847600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:57843400-57847600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:57843600-57847400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:57843800-57847000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:57843800-57847200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:57843800-57847400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:57844000-57846600	Weak transcription	Fetal Brain Male	brain
8	chr1:57844000-57846800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:57844000-57847400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:57844000-57847600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:57844000-57847600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:57844000-57848000	Weak transcription	Fetal Heart	heart
13	chr1:57844200-57847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:57844400-57847200	Weak transcription	Fetal Brain Female	brain
15	chr1:57844800-57847000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:57845200-57847200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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