Variant report

Variant	rs7659254
Chromosome Location	chr4:151117893-151117894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10019650	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12507489	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13107340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1459745	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459746	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459747	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459748	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459749	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1459751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459752	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1563790	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2169086	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2359926	0.88[GIH][hapmap]
rs2359927	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4025876	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4532220	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535718	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535719	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6535720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6843630	0.92[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7658837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7667318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7699202	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7699907	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9307870	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9307871	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9762327	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9997299	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9997489	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999983	0.92[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151097600-151129000	Weak transcription	Lung	lung
2	chr4:151098200-151120000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:151098200-151128000	Weak transcription	Fetal Stomach	stomach
4	chr4:151100000-151127800	Weak transcription	Osteobl	bone
5	chr4:151101600-151127600	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:151103200-151138000	Weak transcription	NH-A	brain
7	chr4:151104200-151127400	Weak transcription	Fetal Brain Female	brain
8	chr4:151104600-151119000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:151108600-151130000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:151108800-151120200	Weak transcription	A549	lung
11	chr4:151108800-151129000	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:151109000-151126400	Weak transcription	Fetal Lung	lung
13	chr4:151112600-151128200	Weak transcription	Left Ventricle	heart
14	chr4:151114000-151118400	Weak transcription	NHLF	lung
15	chr4:151114200-151154200	Weak transcription	Aorta	Aorta
16	chr4:151115400-151127200	Weak transcription	HSMMtube	muscle
17	chr4:151116000-151119400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:151116200-151119200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:151116800-151118200	Enhancers	Brain Germinal Matrix	brain
20	chr4:151117400-151120400	Weak transcription	HSMM	muscle
21	chr4:151117600-151119000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr4:151117800-151119200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:151117800-151128200	Weak transcription	Ovary	ovary

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