Variant report

Variant	rs17117039
Chromosome Location	chr1:58624474-58624475
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10493244	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1106366	0.91[CEU][hapmap]
rs1106367	0.93[CEU][hapmap]
rs11207168	0.91[CEU][hapmap]
rs11207169	0.91[CEU][hapmap]
rs11207170	0.93[CEU][hapmap]
rs11799299	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11799320	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11801568	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11802821	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11809707	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12025945	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12034198	0.98[ASN][1000 genomes]
rs12040062	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12042276	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12048970	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12058945	0.93[CEU][hapmap]
rs1213764	0.93[CEU][hapmap]
rs1213770	0.91[CEU][hapmap]
rs1213771	0.93[CEU][hapmap]
rs12565486	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12565597	0.96[ASN][1000 genomes]
rs1320555	0.91[CEU][hapmap]
rs13374932	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1342875	1.00[CEU][hapmap]
rs1359495	0.93[CEU][hapmap]
rs1416341	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1416343	0.93[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1416344	0.85[EUR][1000 genomes]
rs1416346	1.00[CEU][hapmap]
rs1418765	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17116847	0.91[CEU][hapmap]
rs17116867	0.93[CEU][hapmap]
rs17116869	0.93[CEU][hapmap]
rs17116983	1.00[CEU][hapmap]
rs17116988	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17117013	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17117101	1.00[CEU][hapmap]
rs17117108	0.91[EUR][1000 genomes]
rs17117119	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs17117128	0.85[EUR][1000 genomes]
rs1776184	0.91[CEU][hapmap]
rs1776192	1.00[CEU][hapmap]
rs1832488	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1832489	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1953811	1.00[CEU][hapmap]
rs1992481	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2225949	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2406591	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2797608	1.00[CEU][hapmap]
rs35995264	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3850534	0.87[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs3850535	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3850536	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3861823	0.92[CEU][hapmap]
rs3905539	1.00[CEU][hapmap]
rs4320799	0.93[CEU][hapmap]
rs4406656	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59675977	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59994009	0.92[EUR][1000 genomes]
rs60060991	0.92[EUR][1000 genomes]
rs60112110	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6667829	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs6701275	0.98[ASN][1000 genomes]
rs74074110	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74074991	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74074993	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs74075932	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74075933	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74075935	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74075938	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74076072	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74076075	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74076076	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs74076078	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7522031	0.93[CEU][hapmap]
rs7551611	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs821527	0.91[CEU][hapmap]
rs821528	0.93[CEU][hapmap]
rs821529	0.91[CEU][hapmap]
rs821530	0.86[CEU][hapmap]
rs873989	0.91[CEU][hapmap]
rs946310	0.91[CEU][hapmap]
rs9782935	0.93[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58620800-58625200	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr1:58621200-58625200	Enhancers	GM12878-XiMat	blood
3	chr1:58621200-58626400	Enhancers	Fetal Thymus	thymus
4	chr1:58621200-58626800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:58621200-58629400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr1:58621400-58624600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:58622000-58624800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:58622000-58625400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:58622000-58628800	Weak transcription	Liver	Liver
10	chr1:58622200-58624600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:58622200-58624600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:58622400-58624600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:58622400-58628600	Weak transcription	Left Ventricle	heart
14	chr1:58622600-58624800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:58622800-58624800	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:58623000-58624600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:58623000-58624600	Enhancers	H9 Cell Line	embryonic stem cell
18	chr1:58623000-58624800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr1:58623200-58624600	Enhancers	Fetal Brain Female	brain
20	chr1:58623200-58624800	Enhancers	Fetal Brain Male	brain
21	chr1:58623200-58625000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr1:58623200-58628600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:58623600-58628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:58623800-58624800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:58624000-58624800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:58624200-58624600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:58624200-58627000	Enhancers	Thymus	Thymus
28	chr1:58624400-58627200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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