Variant report

Variant	rs12616629
Chromosome Location	chr2:55944293-55944294
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1084525	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2627769	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2868428	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4452190	0.84[ASN][1000 genomes]
rs62165255	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6748165	0.92[ASN][1000 genomes]
rs7571327	0.95[ASN][1000 genomes]
rs7589673	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs782607	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs782641	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782642	0.81[AMR][1000 genomes]
rs9677174	0.83[EUR][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	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv2762645	chr2:55892248-55963418	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12616629	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55940000-55945600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:55940200-55945600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr2:55940200-55945600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:55940200-55945600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr2:55940200-55945600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr2:55940200-55945800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55940800-55950600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55941800-55948200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:55943200-55948800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:55943400-55945800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:55943600-55945200	Weak transcription	Fetal Intestine Small	intestine
12	chr2:55943800-55944800	Enhancers	HUVEC	blood vessel
13	chr2:55944200-55944400	Enhancers	Fetal Intestine Large	intestine
14	chr2:55944200-55944400	Enhancers	HSMM	muscle

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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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