Variant report

Variant	rs3797900
Chromosome Location	chr5:102898203-102898204
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51976453..51977088-chr5:102898128..102898670,2	Hela-S3	cervix:
2	chr5:102873569..102875593-chr5:102896937..102898488,2	MCF-7	breast:
3	chr15:50978981..50979771-chr5:102897847..102898677,2	Hela-S3	cervix:
4	chr5:102896315..102898883-chr5:107715677..107718329,2	K562	blood:
5	chr5:102896859..102898436-chr5:102902168..102904581,2	MCF-7	breast:
6	chr5:102891995..102895213-chr5:102895551..102898444,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145743	Chromatin interaction
ENSG00000092439	Chromatin interaction
ENSG00000041880	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10057864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061242	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078744	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11737902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750858	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13157247	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356231	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28406419	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672333	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355522	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878912	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880267	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71586376	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73190066	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7707836	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716935	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7723689	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725090	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7730302	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734923	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327885	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882523	chr5:102687151-103342745	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1031600	chr5:102728430-103013575	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1025561	chr5:102744280-103152495	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv537832	chr5:102744280-103152495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1025859	chr5:102744479-103710290	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv537833	chr5:102744479-103710290	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1017730	chr5:102887970-103013575	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv537834	chr5:102887970-103013575	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1017683	chr5:102887970-103110722	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv537835	chr5:102887970-103110722	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3797900	NUDT12	cis	Skin Sun Exposed Lower leg	GTEx
rs3797900	NUDT12	Cis_1M	lymphoblastoid	RTeQTL
rs3797900	NUDT12	cis	parietal	SCAN
rs3797900	NUDT12	cis	lymphoblastoid	seeQTL
rs3797900	NUDT12	cis	multi-tissue	Pritchard
rs3797900	RAB9BP1	cis	parietal	SCAN
rs3797900	ST8SIA4	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:102897000-102898800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:102897000-102898800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:102897000-102899000	Active TSS	NHDF-Ad	bronchial
4	chr5:102897000-102899200	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr5:102897200-102898800	Active TSS	Fetal Intestine Large	intestine
6	chr5:102897200-102898800	Active TSS	Placenta Amnion	Placenta Amnion
7	chr5:102897200-102898800	Active TSS	NHEK	skin
8	chr5:102897200-102899200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:102897200-102899200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:102897200-102899200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr5:102897400-102898800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:102897400-102898800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:102897400-102898800	Active TSS	Muscle Satellite Cultured Cells	--
14	chr5:102897400-102898800	Active TSS	Brain Substantia Nigra	brain
15	chr5:102897400-102898800	Active TSS	Fetal Intestine Small	intestine
16	chr5:102897400-102899000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:102897400-102899000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:102897400-102899000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr5:102897400-102899000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:102897400-102899000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:102897400-102899000	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:102897400-102899000	Active TSS	Fetal Muscle Trunk	muscle
23	chr5:102897400-102899000	Active TSS	Fetal Stomach	stomach
24	chr5:102897400-102899000	Active TSS	Right Ventricle	heart
25	chr5:102897400-102899000	Active TSS	Stomach Mucosa	stomach
26	chr5:102897400-102899000	Active TSS	A549	lung
27	chr5:102897400-102899000	Active TSS	GM12878-XiMat	blood
28	chr5:102897400-102899000	Active TSS	NHLF	lung
29	chr5:102897400-102899200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr5:102897400-102899200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:102897400-102899200	Active TSS	Brain Angular Gyrus	brain
32	chr5:102897400-102899200	Active TSS	Brain Hippocampus Middle	brain
33	chr5:102897400-102899200	Active TSS	Ovary	ovary
34	chr5:102897400-102899200	Active TSS	Psoas Muscle	Psoas
35	chr5:102897400-102899200	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr5:102897400-102899200	Active TSS	Right Atrium	heart
37	chr5:102897400-102899200	Active TSS	HepG2	liver
38	chr5:102897400-102899200	Active TSS	HSMM	muscle
39	chr5:102897600-102898800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr5:102897600-102898800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr5:102897600-102898800	Active TSS	Lung	lung
42	chr5:102897600-102898800	Active TSS	Rectal Mucosa Donor 31	rectum
43	chr5:102897600-102898800	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr5:102897600-102898800	Active TSS	Monocytes-CD14+_RO01746	blood
45	chr5:102897600-102899000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr5:102897600-102899000	Active TSS	H9 Cell Line	embryonic stem cell
47	chr5:102897600-102899000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:102897600-102899000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:102897600-102899000	Active TSS	Brain Anterior Caudate	brain
50	chr5:102897600-102899000	Active TSS	Fetal Heart	heart

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