Variant report

Variant	rs66824127
Chromosome Location	chr3:52551265-52551266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52551111..52554473-chr3:52556873..52560591,3	MCF-7	breast:
2	chr3:52535446..52537192-chr3:52550633..52552577,2	K562	blood:
3	chr3:52541961..52543770-chr3:52548996..52551391,2	K562	blood:
4	chr3:52550660..52553610-chr3:52725143..52727667,2	K562	blood:

Variant related genes	Relation type
ENSG00000163938	Chromatin interaction
ENSG00000222345	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000212452	Chromatin interaction
ENSG00000010327	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1010553	0.87[EUR][1000 genomes]
rs1010554	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11130306	0.86[EUR][1000 genomes]
rs11709284	0.94[EUR][1000 genomes]
rs12489828	0.92[EUR][1000 genomes]
rs13081028	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13303	0.95[EUR][1000 genomes]
rs4282054	0.93[EUR][1000 genomes]
rs66782572	0.82[EUR][1000 genomes]
rs67409736	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6778735	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7614981	0.92[EUR][1000 genomes]
rs7636227	0.82[AMR][1000 genomes];0.96[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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590306	chr3:52536308-52557440	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs66824127	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52530200-52551800	Weak transcription	Esophagus	oesophagus
2	chr3:52530400-52552400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:52530800-52551600	Weak transcription	Fetal Intestine Small	intestine
5	chr3:52533400-52558200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:52533400-52559800	Weak transcription	Liver	Liver
7	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr3:52536600-52564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:52536800-52552600	Strong transcription	Adipose Nuclei	Adipose
12	chr3:52537600-52559800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:52540000-52553600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:52542000-52557400	Weak transcription	Thymus	Thymus
15	chr3:52543800-52552000	Strong transcription	Lung	lung
16	chr3:52544000-52552400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:52544000-52557400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:52545200-52552400	Weak transcription	Right Atrium	heart
19	chr3:52547600-52552600	Weak transcription	Brain Anterior Caudate	brain
20	chr3:52548400-52552400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:52549400-52552400	Weak transcription	Gastric	stomach
22	chr3:52549600-52552200	Weak transcription	Placenta	Placenta
23	chr3:52549800-52553600	Weak transcription	Right Ventricle	heart
24	chr3:52550200-52552600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:52550400-52552000	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:52550600-52566600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:52550800-52558400	Strong transcription	HUVEC	blood vessel
28	chr3:52551000-52552000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:52551000-52554600	Genic enhancers	Spleen	Spleen
30	chr3:52551200-52552200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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