Variant report

Variant	rs13122930
Chromosome Location	chr4:142650413-142650414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1027280	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1027281	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519613	0.83[CHD][hapmap]
rs1057972	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100725	0.85[EUR][1000 genomes]
rs11935530	0.85[EUR][1000 genomes]
rs11940083	0.86[EUR][1000 genomes]
rs12508335	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510030	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13106911	0.80[CHD][hapmap]
rs13112582	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13117878	0.96[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs13123506	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13126364	0.84[EUR][1000 genomes]
rs13130898	0.86[EUR][1000 genomes]
rs13139573	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1493022	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1493025	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1602774	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1602775	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17007610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1873822	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2030326	0.85[EUR][1000 genomes]
rs2090664	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2139383	0.85[EUR][1000 genomes]
rs2291596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2322300	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2322301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2322302	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2857261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3775596	0.83[CHD][hapmap]
rs3775597	0.81[CHD][hapmap]
rs4104674	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4245934	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4254850	0.81[EUR][1000 genomes]
rs4530709	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4597912	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55849760	0.83[EUR][1000 genomes]
rs6537060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6537061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537062	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6537063	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537064	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537070	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6812078	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6819823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6831361	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6847434	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6852617	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677372	0.85[EUR][1000 genomes]
rs932209	0.96[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	esv3448093	chr4:142612197-142704695	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13122930	INPP4B	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142608800-142655000	Weak transcription	Gastric	stomach
2	chr4:142624000-142652000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:142624200-142651000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:142629400-142651000	Weak transcription	Left Ventricle	heart
5	chr4:142629400-142654600	Weak transcription	Esophagus	oesophagus
6	chr4:142629400-142655000	Weak transcription	Spleen	Spleen
7	chr4:142629600-142657600	Weak transcription	Right Ventricle	heart
8	chr4:142634600-142653600	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:142634800-142656200	Weak transcription	Pancreas	Pancrea
10	chr4:142635800-142651600	Weak transcription	NHDF-Ad	bronchial
11	chr4:142635800-142651800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr4:142635800-142651800	Weak transcription	HSMM	muscle
13	chr4:142635800-142651800	Weak transcription	NHLF	lung
14	chr4:142635800-142651800	Weak transcription	Osteobl	bone
15	chr4:142635800-142653600	Weak transcription	HSMMtube	muscle
16	chr4:142637400-142651000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:142638800-142650600	Weak transcription	Liver	Liver
18	chr4:142638800-142651800	Weak transcription	Aorta	Aorta
19	chr4:142639200-142651200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:142639400-142651000	Weak transcription	Adipose Nuclei	Adipose
21	chr4:142639400-142651000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr4:142639600-142651200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:142639600-142655000	Weak transcription	Primary B cells from cord blood	blood
24	chr4:142639600-142657400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr4:142640800-142653000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:142641400-142655000	Weak transcription	Lung	lung
27	chr4:142641800-142651000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:142641800-142654200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr4:142642200-142652400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr4:142643200-142652000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:142643800-142651000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:142644600-142651000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:142644800-142651000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:142644800-142651000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:142644800-142651000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:142644800-142654400	Weak transcription	GM12878-XiMat	blood
37	chr4:142644800-142655800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr4:142645000-142651400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:142645200-142651000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:142645600-142651000	Weak transcription	A549	lung
41	chr4:142646600-142655800	Weak transcription	Small Intestine	intestine
42	chr4:142649800-142655400	Weak transcription	Fetal Intestine Large	intestine
43	chr4:142650400-142651600	Strong transcription	Primary B cells from peripheral blood	blood

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