Variant report

Variant	rs2555417
Chromosome Location	chr2:64520141-64520142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10164841	1.00[JPT][hapmap]
rs10206155	1.00[JPT][hapmap]
rs1030408	0.83[EUR][1000 genomes]
rs1426704	1.00[JPT][hapmap]
rs1534684	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555424	0.88[EUR][1000 genomes]
rs2555429	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2555431	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2555432	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2555447	0.88[EUR][1000 genomes]
rs2555450	0.88[EUR][1000 genomes]
rs2555451	0.87[EUR][1000 genomes]
rs2555454	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2698540	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4459720	1.00[JPT][hapmap]
rs7559505	1.00[JPT][hapmap]
rs7560580	0.88[EUR][1000 genomes]
rs883021	0.87[EUR][1000 genomes]
rs930019	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
11	nsv834244	chr2:64480943-64646259	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2555417	PELI1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64511600-64523200	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:64514400-64523600	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:64515800-64523200	Weak transcription	Fetal Thymus	thymus
4	chr2:64516000-64522400	Weak transcription	Esophagus	oesophagus
5	chr2:64516000-64522800	Weak transcription	Placenta	Placenta
6	chr2:64516000-64524800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:64516400-64522400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr2:64516400-64523400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:64516400-64523600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:64516600-64538000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:64516800-64523000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:64517000-64522400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr2:64517200-64522600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:64517400-64522400	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:64517400-64522600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:64518600-64520200	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:64518600-64523000	Weak transcription	Ovary	ovary
18	chr2:64519200-64527400	Weak transcription	Aorta	Aorta

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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