Variant report

Variant	rs1320996
Chromosome Location	chr6:56100431-56100432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56081250..56083169-chr6:56099533..56102275,2	MCF-7	breast:
2	chr6:56098481..56101054-chr6:56102369..56105137,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10081146	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1022539	0.82[AFR][1000 genomes]
rs11970688	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12190324	0.90[AFR][1000 genomes]
rs13193925	0.81[AFR][1000 genomes]
rs13209836	0.83[AFR][1000 genomes]
rs1474698	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1925139	0.82[AFR][1000 genomes]
rs1925144	0.90[AFR][1000 genomes]
rs1925145	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1925148	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1925152	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1925153	0.96[AFR][1000 genomes]
rs1980487	0.82[AFR][1000 genomes]
rs1998700	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2038149	0.83[AFR][1000 genomes]
rs2038150	0.83[AFR][1000 genomes]
rs2223598	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3846922	0.90[AFR][1000 genomes]
rs3846924	0.91[AFR][1000 genomes]
rs3846925	0.92[AFR][1000 genomes]
rs3846926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3899394	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4119567	0.83[AFR][1000 genomes]
rs4126555	0.90[AFR][1000 genomes]
rs4126556	0.90[AFR][1000 genomes]
rs4126557	0.90[AFR][1000 genomes]
rs4126558	0.90[AFR][1000 genomes]
rs4140573	0.83[AFR][1000 genomes]
rs4140574	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140575	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4310058	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4490668	0.83[AFR][1000 genomes]
rs4712116	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4712120	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4715583	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715584	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4715589	0.83[AFR][1000 genomes]
rs4715590	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4715594	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4715596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6459130	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6459134	0.82[AFR][1000 genomes]
rs6904431	0.90[AFR][1000 genomes]
rs6920461	0.83[AFR][1000 genomes]
rs6930358	0.81[AMR][1000 genomes]
rs6934945	0.83[AFR][1000 genomes]
rs6935200	0.87[AFR][1000 genomes]
rs6936386	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs761104	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs761105	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs764517	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7741903	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7762422	0.89[AFR][1000 genomes]
rs7776118	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs926534	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs926535	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9296832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296833	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9357893	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9357897	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9367678	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9382584	0.81[EUR][1000 genomes]
rs9382595	0.90[AFR][1000 genomes]
rs9396176	0.82[AFR][1000 genomes]
rs9396181	0.87[AFR][1000 genomes]
rs9396183	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9475583	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9475586	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9475641	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1320996	COL21A1	cis	Nerve Tibial	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56082200-56104800	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:56096600-56105400	Weak transcription	Psoas Muscle	Psoas
3	chr6:56097800-56105400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr6:56098000-56106200	Weak transcription	Fetal Lung	lung
5	chr6:56099400-56101800	Enhancers	Colon Smooth Muscle	Colon
6	chr6:56099800-56100600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:56099800-56100600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:56099800-56100600	Enhancers	Muscle Satellite Cultured Cells	--
9	chr6:56100000-56100600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:56100000-56100600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:56100000-56100600	Enhancers	Fetal Heart	heart
12	chr6:56100000-56101200	Weak transcription	Esophagus	oesophagus
13	chr6:56100000-56101200	Enhancers	Stomach Smooth Muscle	stomach
14	chr6:56100000-56103400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr6:56100000-56105400	Weak transcription	Aorta	Aorta
16	chr6:56100200-56111600	Weak transcription	Right Atrium	heart
17	chr6:56100400-56100800	Weak transcription	Brain Anterior Caudate	brain
18	chr6:56100400-56100800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:56100400-56105600	Weak transcription	Fetal Stomach	stomach
20	chr6:56100400-56107400	Weak transcription	A549	lung

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