Variant report

Variant	rs17117046
Chromosome Location	chr1:58624873-58624874
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10493243	1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12021839	0.89[JPT][hapmap];1.00[EUR][1000 genomes]
rs12022240	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12025951	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12036406	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037550	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12037749	0.81[ASN][1000 genomes]
rs12040992	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12042296	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12042368	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12043154	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12045007	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046343	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12046993	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12049240	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17117004	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2039733	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095817	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4912182	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4912308	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59962900	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60227124	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60974573	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs637081	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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:24 , 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	chr1:58622000-58625400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:58622000-58628800	Weak transcription	Liver	Liver
8	chr1:58622400-58628600	Weak transcription	Left Ventricle	heart
9	chr1:58623200-58625000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:58623200-58628600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:58623600-58628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:58624200-58627000	Enhancers	Thymus	Thymus
13	chr1:58624400-58627200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr1:58624600-58626600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:58624600-58626600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:58624600-58627800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:58624600-58628600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:58624600-58633800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:58624600-58634600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:58624800-58625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:58624800-58626200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:58624800-58630200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:58624800-58630800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:58624800-58634200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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