Variant report

Variant	rs3925117
Chromosome Location	chr4:151120849-151120850
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:151102342..151104330-chr4:151119995..151122046,2	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11727182	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459750	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs17503402	1.00[ASW][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1993656	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs34681163	0.87[ASN][1000 genomes]
rs6535725	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9683765	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats 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	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3925117	ARFIP1	cis	cerebellum	SCAN
rs3925117	DCLK2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151097600-151129000	Weak transcription	Lung	lung
2	chr4:151098200-151128000	Weak transcription	Fetal Stomach	stomach
3	chr4:151100000-151127800	Weak transcription	Osteobl	bone
4	chr4:151101600-151127600	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:151103200-151138000	Weak transcription	NH-A	brain
6	chr4:151104200-151127400	Weak transcription	Fetal Brain Female	brain
7	chr4:151108600-151130000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr4:151108800-151129000	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:151109000-151126400	Weak transcription	Fetal Lung	lung
10	chr4:151112600-151128200	Weak transcription	Left Ventricle	heart
11	chr4:151114200-151154200	Weak transcription	Aorta	Aorta
12	chr4:151115400-151127200	Weak transcription	HSMMtube	muscle
13	chr4:151117800-151128200	Weak transcription	Ovary	ovary
14	chr4:151118000-151127200	Weak transcription	Brain Anterior Caudate	brain
15	chr4:151118200-151127000	Weak transcription	Brain Germinal Matrix	brain
16	chr4:151118400-151128200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:151119000-151122200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:151119000-151122800	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:151119200-151121400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:151119200-151123200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr4:151119800-151121600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:151120000-151132200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:151120400-151121200	Strong transcription	HSMM	muscle
24	chr4:151120400-151128200	Weak transcription	A549	lung
25	chr4:151120400-151129000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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