Variant report

Variant	rs28430857
Chromosome Location	chr4:99793417-99793418
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	chr4:99790542..99794332-chr4:99796415..99799173,3	MCF-7	breast:
2	chr4:99788669..99795138-chr4:99795530..99800128,7	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADH5-6	chr4:99792836-99795886	NONHSAT097499

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10007957	0.97[ASN][1000 genomes]
rs10008093	0.97[ASN][1000 genomes]
rs10010610	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10011791	0.90[ASN][1000 genomes]
rs10019506	0.94[ASN][1000 genomes]
rs10020687	0.98[ASN][1000 genomes]
rs10022521	0.94[ASN][1000 genomes]
rs10032966	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10212891	0.89[ASN][1000 genomes]
rs1036946	0.99[ASN][1000 genomes]
rs10433891	0.99[ASN][1000 genomes]
rs10433976	0.86[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10461135	0.97[ASN][1000 genomes]
rs10470955	0.99[ASN][1000 genomes]
rs10516437	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11725932	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11728783	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11737130	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11737186	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1230147	0.89[ASN][1000 genomes]
rs1230149	0.88[ASN][1000 genomes]
rs1230150	0.88[ASN][1000 genomes]
rs1230152	0.89[ASN][1000 genomes]
rs1230189	0.80[ASN][1000 genomes]
rs17028238	0.97[ASN][1000 genomes]
rs17028241	0.97[ASN][1000 genomes]
rs17028244	0.97[ASN][1000 genomes]
rs17028293	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17550514	0.97[ASN][1000 genomes]
rs2602889	0.84[ASN][1000 genomes]
rs28367437	0.94[ASN][1000 genomes]
rs28376834	0.94[ASN][1000 genomes]
rs28473608	0.97[ASN][1000 genomes]
rs28499420	0.94[ASN][1000 genomes]
rs28529446	0.94[ASN][1000 genomes]
rs28575093	0.99[ASN][1000 genomes]
rs28577966	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28589528	0.90[ASN][1000 genomes]
rs28613604	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28622595	0.90[ASN][1000 genomes]
rs28633499	0.97[ASN][1000 genomes]
rs3133161	0.89[ASN][1000 genomes]
rs35447189	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699686	0.92[AMR][1000 genomes]
rs4699687	0.92[AMR][1000 genomes]
rs60120090	0.97[ASN][1000 genomes]
rs60658326	0.97[ASN][1000 genomes]
rs6532774	0.97[ASN][1000 genomes]
rs6815444	0.97[ASN][1000 genomes]
rs6830125	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6841295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846266	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846475	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72677504	0.97[ASN][1000 genomes]
rs72692622	0.99[ASN][1000 genomes]
rs7660937	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7661487	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7664964	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7666015	0.89[ASN][1000 genomes]
rs7671306	0.99[ASN][1000 genomes]
rs7671453	0.99[ASN][1000 genomes]
rs7674319	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676504	0.99[ASN][1000 genomes]
rs7679685	0.90[ASN][1000 genomes]
rs7684964	0.94[ASN][1000 genomes]
rs7696573	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696584	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697071	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9332467	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994636	0.99[ASN][1000 genomes]
rs9995478	0.89[ASN][1000 genomes]
rs9996959	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9999702	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv879655	chr4:99783733-99843113	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99785400-99798800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr4:99790800-99805400	Weak transcription	Fetal Lung	lung
3	chr4:99791200-99798800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:99792200-99795400	Enhancers	K562	blood
5	chr4:99792400-99794800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr4:99792400-99825000	Weak transcription	Gastric	stomach
7	chr4:99792600-99794200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:99792600-99804000	Weak transcription	HUVEC	blood vessel
9	chr4:99792800-99794000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:99792800-99797600	Weak transcription	HSMM	muscle
11	chr4:99792800-99799000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr4:99793000-99800800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr4:99793400-99803000	Weak transcription	Stomach Mucosa	stomach

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