Variant report

Variant	rs181274
Chromosome Location	chr3:52233861-52233862
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52230039..52234196-chr3:52236127..52242387,6	K562	blood:
2	chr3:52186178..52189000-chr3:52232033..52234935,2	K562	blood:

Variant related genes	Relation type
ENSG00000023330	Chromatin interaction
ENSG00000164087	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs104903	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1060330	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs11712164	0.95[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs11717383	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs164640	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs187084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs352139	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs352140	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs352158	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs352161	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs352162	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352163	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs352165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352169	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352170	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352171	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs353547	0.81[CHB][hapmap]
rs353551	0.90[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs411457	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs524986	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs610060	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs614288	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6445358	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6802320	0.87[ASN][1000 genomes]
rs730050	0.81[JPT][hapmap]
rs7614727	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7622851	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv876786	chr3:52041566-52236762	Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
5	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
8	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
9	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs181274	FLJ12442	cis	multi-tissue	Pritchard
rs181274	NT5DC2	cis	multi-tissue	Pritchard
rs181274	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52233000-52234400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr3:52233000-52234400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:52233000-52234600	Transcr. at gene 5' and 3'	Liver	Liver
4	chr3:52233000-52235200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:52233000-52235400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:52233000-52236200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:52233000-52236400	Weak transcription	Aorta	Aorta
8	chr3:52233000-52241600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:52233000-52245200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr3:52233200-52234400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr3:52233200-52234800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
12	chr3:52233200-52235600	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr3:52233200-52235800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr3:52233400-52234000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:52233400-52234200	Weak transcription	NH-A	brain
16	chr3:52233400-52234600	Weak transcription	HSMM	muscle
17	chr3:52233400-52234800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:52233400-52234800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr3:52233400-52235200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr3:52233400-52235400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr3:52233400-52235800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:52233400-52236400	Weak transcription	Ovary	ovary
23	chr3:52233400-52236600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:52233400-52237000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:52233400-52237800	Genic enhancers	Primary B cells from cord blood	blood
26	chr3:52233400-52249600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:52233400-52249800	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:52233400-52250000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:52233400-52250000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr3:52233600-52234000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:52233600-52234200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:52233600-52234200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:52233600-52234400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:52233600-52234400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:52233600-52234400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:52233600-52234600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:52233600-52234600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:52233600-52234600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr3:52233600-52234600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:52233600-52234600	Weak transcription	A549	lung
41	chr3:52233600-52234800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:52233600-52234800	Weak transcription	Fetal Brain Female	brain
43	chr3:52233600-52235200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:52233600-52235200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:52233600-52235200	Weak transcription	Fetal Kidney	kidney
46	chr3:52233600-52235200	Weak transcription	K562	blood
47	chr3:52233600-52235200	Weak transcription	NHDF-Ad	bronchial
48	chr3:52233600-52235400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:52233600-52235400	Weak transcription	Brain Germinal Matrix	brain
50	chr3:52233600-52235600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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