Variant report

Variant	rs17752868
Chromosome Location	chr2:64285521-64285522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS54-3	chr2:64283928-64286123	NONHSAT071084
2	lnc-VPS54-3	chr2:64283928-64286123	refGeneNc_4218_NR_033837

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12993544	1.00[YRI][hapmap]
rs13032357	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17701941	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17753018	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17753048	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2080650	0.81[EUR][1000 genomes]
rs2287361	1.00[YRI][hapmap]
rs34737670	0.83[ASN][1000 genomes]
rs4544421	1.00[YRI][hapmap]
rs4599090	1.00[YRI][hapmap]
rs71422401	0.83[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	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64277400-64291200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:64280000-64290600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:64281600-64290800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr2:64281600-64291200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:64282000-64290200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:64282000-64290600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:64282400-64289200	Weak transcription	GM12878-XiMat	blood
8	chr2:64282800-64290200	Weak transcription	Thymus	Thymus
9	chr2:64283000-64285600	Weak transcription	Placenta	Placenta
10	chr2:64284000-64290400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:64284200-64289600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:64284400-64289600	Weak transcription	NHEK	skin
13	chr2:64284600-64286600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:64285200-64285600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:64285400-64285600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:64285400-64285600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:64285400-64285800	Enhancers	H9 Cell Line	embryonic stem cell
18	chr2:64285400-64285800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:64285400-64285800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:64285400-64285800	Enhancers	Fetal Thymus	thymus

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