Variant report

Variant	rs13117878
Chromosome Location	chr4:142599222-142599223
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:142597917..142599701-chr4:142616061..142617565,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1027280	0.88[EUR][1000 genomes]
rs1027281	0.87[EUR][1000 genomes]
rs1057972	0.87[EUR][1000 genomes]
rs12508335	0.88[EUR][1000 genomes]
rs12508866	0.89[CHD][hapmap];0.84[JPT][hapmap]
rs12510030	0.89[EUR][1000 genomes]
rs13112582	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs13122930	0.96[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs13123506	0.91[EUR][1000 genomes]
rs13126364	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13139573	0.96[CEU][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs1493022	0.87[EUR][1000 genomes]
rs1493025	0.87[EUR][1000 genomes]
rs1519551	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1602774	0.86[EUR][1000 genomes]
rs1602775	0.86[EUR][1000 genomes]
rs17007610	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs1873822	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs2030326	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2090664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2139383	0.96[EUR][1000 genomes]
rs2291596	0.96[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2322300	0.90[EUR][1000 genomes]
rs2322301	0.96[CEU][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs2322302	0.86[EUR][1000 genomes]
rs2857261	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4104674	0.87[EUR][1000 genomes]
rs4245934	0.87[EUR][1000 genomes]
rs4530709	0.91[EUR][1000 genomes]
rs4597912	0.86[EUR][1000 genomes]
rs55849760	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6537060	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6537061	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6537062	0.83[EUR][1000 genomes]
rs6537063	0.86[EUR][1000 genomes]
rs6537064	0.85[EUR][1000 genomes]
rs6537070	0.87[EUR][1000 genomes]
rs6812078	0.87[EUR][1000 genomes]
rs6819823	0.96[CEU][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs6831361	0.86[EUR][1000 genomes]
rs6847434	0.91[EUR][1000 genomes]
rs6852617	0.86[EUR][1000 genomes]
rs932209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030822	chr4:142487721-142706053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13117878	INPP4B	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142583400-142634600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:142589800-142600000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:142597400-142599400	Enhancers	Fetal Intestine Large	intestine
4	chr4:142597400-142600000	Enhancers	A549	lung
5	chr4:142597800-142599400	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr4:142597800-142599800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:142597800-142607600	Weak transcription	Small Intestine	intestine
8	chr4:142598000-142600200	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr4:142598200-142599400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr4:142598600-142601800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:142599000-142599400	Enhancers	Fetal Heart	heart
12	chr4:142599000-142599400	Enhancers	Psoas Muscle	Psoas
13	chr4:142599000-142599800	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr4:142599000-142601200	Weak transcription	Fetal Intestine Small	intestine
15	chr4:142599200-142599400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr4:142599200-142599600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:142599200-142600000	Weak transcription	NHDF-Ad	bronchial
18	chr4:142599200-142600800	Weak transcription	Stomach Mucosa	stomach
19	chr4:142599200-142605000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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