Variant report

Variant	rs25976
Chromosome Location	chr5:106835010-106835011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs152558	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs152560	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs152562	0.82[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs25966	0.81[GIH][hapmap];0.82[MEX][hapmap]
rs25997	0.91[MEX][hapmap]
rs31717	0.84[GIH][hapmap]
rs32003	0.81[ASN][1000 genomes]
rs32004	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs32013	0.94[CHB][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030118	chr5:106006097-106847949	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
2	nsv1034276	chr5:106461538-106944163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537851	chr5:106461538-106944163	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv34018	chr5:106720912-107110506	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs25976	NUDT12	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:106808400-106837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:106820600-106838200	Weak transcription	Fetal Brain Male	brain
3	chr5:106823000-106837600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:106823200-106837800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:106823400-106835400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:106823600-106837800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:106825800-106835400	Weak transcription	HUVEC	blood vessel
8	chr5:106826600-106838400	Weak transcription	Left Ventricle	heart
9	chr5:106829600-106837600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:106829800-106835800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr5:106830600-106837800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:106832600-106837800	Weak transcription	HSMM	muscle
13	chr5:106833200-106839400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr5:106834000-106836400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:106834000-106836800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr5:106834000-106837000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:106834200-106835800	Enhancers	H9 Cell Line	embryonic stem cell
18	chr5:106834200-106836800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr5:106834200-106836800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr5:106834200-106837000	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr5:106834200-106837400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:106834200-106838200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:106834200-106840400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr5:106834400-106836200	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr5:106834400-106836200	Enhancers	Fetal Heart	heart
26	chr5:106834400-106836600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr5:106834400-106840000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr5:106834400-106848600	Weak transcription	HMEC	breast
29	chr5:106834600-106838800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr5:106834800-106836000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:106834800-106836000	Enhancers	Brain Germinal Matrix	brain
32	chr5:106834800-106836200	Weak transcription	Stomach Mucosa	stomach
33	chr5:106835000-106835400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr5:106835000-106835400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr5:106835000-106835800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:106835000-106836800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr5:106835000-106836800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:106835000-106838000	Enhancers	A549	lung

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