Variant report

Variant	rs1540403
Chromosome Location	chr4:96070299-96070300
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10004711	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10155123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10155222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10212627	0.96[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10516958	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11097456	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11097457	0.85[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11097458	0.96[CEU][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12506402	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12640643	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12644188	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12650281	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13139538	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1365691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1369085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1434535	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1434536	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1434538	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1434539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1434544	0.81[EUR][1000 genomes]
rs17348139	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1813074	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1836261	0.81[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1863654	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865379	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1966548	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs1970801	0.81[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2114533	0.89[EUR][1000 genomes]
rs2162450	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241743	0.84[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs2241744	0.96[CEU][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2289044	0.85[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2865397	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs3755876	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3775042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3796437	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3796439	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs3796443	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3821964	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs3857227	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3857228	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58399580	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60472405	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6815969	0.90[EUR][1000 genomes]
rs7664562	0.85[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7694131	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7694531	0.81[CEU][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs965823	0.92[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs975608	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs989383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[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	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv492312	chr4:95823124-96128327	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv830011	chr4:95947560-96103934	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv594907	chr4:95975470-96170439	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:96034200-96079200	Weak transcription	Fetal Kidney	kidney
2	chr4:96051400-96075800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr4:96054200-96084000	Weak transcription	A549	lung
4	chr4:96059800-96100400	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr4:96061000-96079800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:96061200-96074400	Weak transcription	Fetal Muscle Leg	muscle
7	chr4:96061200-96076200	Weak transcription	Thymus	Thymus
8	chr4:96061200-96079000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:96061200-96079200	Weak transcription	Fetal Stomach	stomach
10	chr4:96061200-96079800	Weak transcription	Pancreas	Pancrea
11	chr4:96061200-96088800	Weak transcription	Aorta	Aorta
12	chr4:96061200-96088800	Weak transcription	Ovary	ovary
13	chr4:96061800-96079000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:96063600-96076200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:96063600-96076200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:96063800-96077800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:96064800-96075600	Weak transcription	Fetal Thymus	thymus
18	chr4:96064800-96078800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:96066400-96072400	Strong transcription	Dnd41	blood
20	chr4:96069600-96070400	Enhancers	Primary T cells from cord blood	blood
21	chr4:96069800-96071200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:96070000-96070400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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