Variant report

Variant	rs614288
Chromosome Location	chr3:52220203-52220204
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52219244..52220866-chr3:52225741..52228614,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242849	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs104903	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1060330	0.81[CHB][hapmap]
rs11712164	0.95[CHB][hapmap]
rs11717383	0.81[CHB][hapmap]
rs164640	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs181274	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]
rs187084	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs34656997	0.83[ASN][1000 genomes]
rs352139	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs352140	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs352158	0.92[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352161	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs352162	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs352163	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352165	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs352166	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs352167	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs352168	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs352169	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs352170	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs352171	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs353547	0.81[CHB][hapmap]
rs353551	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs411457	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs524986	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs610060	0.81[CHB][hapmap]
rs6445358	0.81[CHB][hapmap]
rs7614727	0.81[CHB][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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs614288	NT5DC2	cis	lymphoblastoid	seeQTL
rs614288	NT5DC2	cis	cerebellum	SCAN
rs614288	GLYCTK	cis	parietal	SCAN
rs614288	FLJ12442	cis	multi-tissue	Pritchard
rs614288	RBM6	cis	cerebellum	SCAN
rs614288	NEK4	cis	cerebellum	SCAN
rs614288	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs614288	SEMA3G	cis	cerebellum	SCAN
rs614288	DNAH1	cis	cerebellum	SCAN
rs614288	GNL3	cis	cerebellum	SCAN
rs614288	NEK4	cis	parietal	SCAN
rs614288	SPCS1	cis	parietal	SCAN
rs614288	GNL3	cis	parietal	SCAN
rs614288	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs614288	ITIH4	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52212000-52222400	Weak transcription	Stomach Mucosa	stomach
2	chr3:52212800-52223800	Weak transcription	Esophagus	oesophagus
3	chr3:52214600-52221000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr3:52215800-52224200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:52216600-52223600	Enhancers	HepG2	liver
6	chr3:52217200-52224200	Weak transcription	Right Atrium	heart
7	chr3:52217400-52224800	Weak transcription	Spleen	Spleen
8	chr3:52217600-52231600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:52218200-52220400	Weak transcription	Liver	Liver
10	chr3:52218400-52220600	Weak transcription	Placenta	Placenta
11	chr3:52218400-52222200	Weak transcription	Fetal Intestine Large	intestine
12	chr3:52218400-52223800	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:52218600-52224800	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr3:52218800-52229800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:52219000-52223000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:52219200-52222200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:52219200-52224000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:52219200-52224200	Weak transcription	Adipose Nuclei	Adipose
19	chr3:52219200-52224200	Weak transcription	Left Ventricle	heart
20	chr3:52219400-52220600	Enhancers	Primary hematopoietic stem cells	blood
21	chr3:52219400-52225000	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr3:52219600-52225200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr3:52219800-52220800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:52220000-52220800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:52220200-52220400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:52220200-52220400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:52220200-52222400	Weak transcription	K562	blood
28	chr3:52220200-52224600	Weak transcription	Right Ventricle	heart
29	chr3:52220200-52230000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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