Variant report

Variant	rs1813074
Chromosome Location	chr4:96087973-96087974
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPGDS-5	chr4:96083659-96088750	NONHSAT097459

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

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

rs_ID	r²[population]
rs10004711	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10155123	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10155222	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10212627	0.96[CEU][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10516958	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11097456	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11097457	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs11097458	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12506402	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12640643	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12644188	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12650281	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13139538	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1365691	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1369085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1434535	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1434536	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1434538	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1434539	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1540403	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]
rs17348139	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1836261	0.81[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1863654	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1966548	0.85[CEU][hapmap]
rs1970801	0.82[CEU][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2114533	0.84[EUR][1000 genomes]
rs2162450	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241743	0.85[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241744	0.96[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2289044	0.90[JPT][hapmap]
rs2865397	0.82[CEU][hapmap]
rs3755876	0.96[CEU][hapmap];0.80[CHD][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3775042	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3796437	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3796443	0.96[CEU][hapmap];0.80[CHD][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3796462	0.81[CHD][hapmap]
rs3821964	0.82[CEU][hapmap]
rs3857227	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3857228	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58399580	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60472405	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6815969	0.85[EUR][1000 genomes]
rs7664562	0.90[JPT][hapmap]
rs7693146	0.84[ASN][1000 genomes]
rs7694131	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7694531	0.82[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs965823	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs975608	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs989383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9992669	0.81[EUR][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:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:96059800-96100400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:96061200-96088800	Weak transcription	Aorta	Aorta
3	chr4:96061200-96088800	Weak transcription	Ovary	ovary
4	chr4:96077200-96088200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:96079400-96088600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:96079400-96089000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:96080400-96088200	Weak transcription	Brain Angular Gyrus	brain
8	chr4:96080400-96098600	Weak transcription	Fetal Kidney	kidney
9	chr4:96081200-96091000	Weak transcription	Fetal Thymus	thymus
10	chr4:96084400-96090200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr4:96084600-96090200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:96084600-96111800	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:96084800-96090800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr4:96084800-96099800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:96085200-96088600	Weak transcription	Fetal Stomach	stomach
16	chr4:96085200-96090200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:96086400-96088200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:96086600-96088000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:96087400-96088800	Enhancers	Brain Substantia Nigra	brain
20	chr4:96087400-96089200	Enhancers	Fetal Lung	lung
21	chr4:96087400-96089400	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:96087400-96089400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr4:96087400-96089800	Enhancers	Brain Hippocampus Middle	brain
24	chr4:96087600-96088200	Enhancers	Primary T cells from cord blood	blood
25	chr4:96087600-96107000	Weak transcription	A549	lung
26	chr4:96087800-96089600	Weak transcription	Brain Anterior Caudate	brain
27	chr4:96087800-96090200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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