Variant report

Variant	rs1316970
Chromosome Location	chr5:89919363-89919364
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:89908105..89911531-chr5:89917925..89920470,3	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10043564	0.81[ASN][1000 genomes]
rs12186867	0.81[ASN][1000 genomes]
rs12653924	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs149321	0.97[ASN][1000 genomes]
rs154566	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1673381	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2366772	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2366775	0.99[ASN][1000 genomes]
rs250366	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs250369	0.94[ASN][1000 genomes]
rs27196	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27197	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs28480058	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3112773	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4588621	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5028525	0.99[ASN][1000 genomes]
rs567441	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs649449	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs656679	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6891287	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6891840	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6892132	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs908818	0.82[ASN][1000 genomes]
rs9283789	0.92[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	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats 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	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1316970	LYSMD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89909800-89919600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr5:89909800-89923200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr5:89909800-89923200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:89909800-89926400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:89909800-89928800	Weak transcription	Fetal Brain Female	brain
6	chr5:89910000-89927000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr5:89910000-89928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:89914000-89919400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:89914200-89919400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:89914200-89920800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:89914200-89927000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:89914200-89928600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:89916800-89925600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:89917000-89927000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:89917400-89920600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr5:89917400-89923200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:89917400-89926200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:89917800-89922000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:89918000-89950600	Weak transcription	Pancreas	Pancrea
20	chr5:89918200-89924400	Weak transcription	K562	blood
21	chr5:89918200-89925800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:89919000-89925600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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