Variant report

Variant	rs1779985
Chromosome Location	chr1:247129945-247129946
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1039009	0.82[MEX][hapmap]
rs1039010	0.86[MEX][hapmap]
rs12722828	0.87[JPT][hapmap]
rs1622905	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1691245	0.91[MEX][hapmap]
rs1691246	0.91[MEX][hapmap]
rs1691250	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1779958	0.87[JPT][hapmap];0.95[MEX][hapmap]
rs1779959	0.87[JPT][hapmap];0.95[MEX][hapmap]
rs1779962	0.87[JPT][hapmap];0.95[MEX][hapmap];0.81[EUR][1000 genomes]
rs1779984	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2642964	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2642977	0.82[ASW][hapmap];0.85[MEX][hapmap]
rs2642982	0.87[JPT][hapmap]
rs2642983	0.87[JPT][hapmap];0.95[MEX][hapmap]
rs2800214	0.82[MEX][hapmap]
rs2800216	0.81[EUR][1000 genomes]
rs2818887	0.81[EUR][1000 genomes]
rs2818890	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971282	0.83[CHB][hapmap]
rs768197	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv873425	chr1:247069514-247156066	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv873426	chr1:247069514-247162628	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
11	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
12	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
13	nsv524007	chr1:247098587-247162658	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1002054	chr1:247108896-247161897	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv535419	chr1:247108896-247161897	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
17	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1779985	TRIM58	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247096000-247130400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:247096000-247131600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:247096000-247131800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:247107800-247130200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr1:247111400-247130200	Weak transcription	HSMM	muscle
6	chr1:247111400-247131000	Weak transcription	HepG2	liver
7	chr1:247111400-247131400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:247113400-247130600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:247118000-247130600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:247120200-247130600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:247121800-247130200	Strong transcription	Dnd41	blood
12	chr1:247122000-247130600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:247125400-247149400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:247125600-247130600	Weak transcription	Brain Germinal Matrix	brain
15	chr1:247126200-247131400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:247126400-247135800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:247126600-247130200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:247127800-247130600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:247127800-247130600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:247127800-247130600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr1:247127800-247130600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:247128600-247130600	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr1:247128600-247132400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr1:247128800-247131000	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr1:247129000-247131200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:247129200-247131400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:247129400-247132200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:247129600-247132200	Weak transcription	Fetal Lung	lung
29	chr1:247129800-247130200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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