Variant report

Variant	rs2347252
Chromosome Location	chr3:138095525-138095526
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138089900..138093622-chr3:138093776..138096723,3	MCF-7	breast:
2	chr3:138094416..138096515-chr3:138105748..138108016,2	MCF-7	breast:
3	chr3:138084125..138087091-chr3:138095064..138097156,2	K562	blood:
4	chr3:138093996..138096598-chr4:123678799..123680914,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10513053	0.89[JPT][hapmap]
rs1199337	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1199338	1.00[CEU][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs12695685	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074317	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13079209	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13080413	1.00[ASN][1000 genomes]
rs13083299	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096934	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324341	0.93[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs1720819	0.93[GIH][hapmap]
rs185244	0.93[EUR][1000 genomes]
rs2279241	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291127	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293251	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306374	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34078858	0.84[ASN][1000 genomes]
rs34140440	0.90[ASN][1000 genomes]
rs34568901	1.00[ASN][1000 genomes]
rs34905952	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3732837	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773750	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs59217491	0.84[ASN][1000 genomes]
rs6807945	0.93[CEU][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs9818870	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828345	1.00[JPT][hapmap]
rs9848655	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851766	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864898	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872754	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv528349	chr3:138025396-138132393	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1796956	chr3:138051423-138122781	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv1848610	chr3:138051423-138133412	Bivalent Enhancer Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1797142	chr3:138087467-138122781	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1845560	chr3:138087467-138133412	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2347252	RBP1	cis	parietal	SCAN
rs2347252	TRIM42	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138070000-138096600	Weak transcription	Fetal Brain Male	brain
2	chr3:138071200-138096600	Weak transcription	Aorta	Aorta
3	chr3:138074200-138095600	Enhancers	Fetal Heart	heart
4	chr3:138076000-138108200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:138078600-138100600	Weak transcription	NH-A	brain
6	chr3:138079600-138095600	Weak transcription	Fetal Brain Female	brain
7	chr3:138080200-138096400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:138081600-138108200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:138083000-138100400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:138083200-138100600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:138085200-138100000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:138085800-138096200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:138086200-138100400	Weak transcription	HepG2	liver
14	chr3:138086800-138100600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:138087000-138096000	Weak transcription	Placenta	Placenta
16	chr3:138087200-138097000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:138087200-138100000	Weak transcription	Pancreas	Pancrea
18	chr3:138087200-138100600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:138087400-138097000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:138089200-138096200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:138089200-138100000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:138089200-138100800	Weak transcription	Fetal Lung	lung
23	chr3:138089400-138100000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:138089400-138100000	Weak transcription	Brain Angular Gyrus	brain
25	chr3:138089400-138102400	Weak transcription	Spleen	Spleen
26	chr3:138089600-138097600	Weak transcription	Brain Substantia Nigra	brain
27	chr3:138089600-138100200	Weak transcription	Lung	lung
28	chr3:138090400-138119400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:138091000-138098000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr3:138091200-138096400	Weak transcription	Brain Anterior Caudate	brain
31	chr3:138091200-138100400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:138091400-138096600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:138091400-138100800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:138091600-138096000	Weak transcription	Right Ventricle	heart
35	chr3:138091600-138098600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:138091800-138098000	Strong transcription	HSMM	muscle
37	chr3:138092000-138096000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:138092000-138096400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:138092200-138096000	Weak transcription	Fetal Stomach	stomach
40	chr3:138092200-138096800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr3:138093400-138095800	Genic enhancers	HSMMtube	muscle
42	chr3:138093400-138097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:138093600-138095800	Enhancers	Ovary	ovary
44	chr3:138093600-138100400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:138093800-138100000	Weak transcription	Colon Smooth Muscle	Colon
46	chr3:138093800-138100400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr3:138094000-138097000	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:138094000-138104800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:138094200-138096800	Weak transcription	Osteobl	bone
50	chr3:138094400-138097200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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