Variant report

Variant	rs4428939
Chromosome Location	chr1:85861564-85861565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1006989	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10489510	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10747318	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782549	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873701	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873702	0.84[AFR][1000 genomes]
rs11161611	0.85[AFR][1000 genomes]
rs12022248	0.98[ASN][1000 genomes]
rs12029221	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12033483	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12034249	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12035116	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12038426	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12042780	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12047189	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1261681	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1342323	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1357635	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1357636	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391556	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1523995	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554597	0.83[AFR][1000 genomes]
rs1608537	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17384213	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17388696	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1965876	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011825	0.84[AFR][1000 genomes]
rs2016104	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037594	0.89[EUR][1000 genomes]
rs2064510	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124139	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124140	0.84[ASN][1000 genomes]
rs2177461	0.86[AFR][1000 genomes]
rs2207368	0.84[AFR][1000 genomes]
rs2300633	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2389948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851268	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3949301	0.86[AFR][1000 genomes]
rs4512701	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4631749	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4949889	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949897	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4949898	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4949899	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs499869	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs539714	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs600098	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs604974	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs631817	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6420965	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6576767	0.82[AFR][1000 genomes]
rs659070	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6657817	0.83[AFR][1000 genomes]
rs6671599	0.80[AFR][1000 genomes]
rs6672870	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704103	0.85[AFR][1000 genomes]
rs67611930	0.84[AFR][1000 genomes]
rs72722663	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72722671	0.90[ASN][1000 genomes]
rs72722691	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72722692	0.86[AMR][1000 genomes]
rs72724606	0.83[AFR][1000 genomes]
rs72724608	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs731194	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7515261	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7539738	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7546931	0.83[AFR][1000 genomes]
rs7555670	0.89[EUR][1000 genomes]
rs990916	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1008877	chr1:85843238-85897570	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3393958	chr1:85857980-85874598	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85839800-85864200	Weak transcription	Aorta	Aorta
2	chr1:85845000-85870000	Weak transcription	HSMMtube	muscle
3	chr1:85849400-85861600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:85849400-85863400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:85850800-85863600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:85852400-85863400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:85852400-85864200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:85853200-85861800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:85853600-85861800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:85853800-85861600	Weak transcription	NHDF-Ad	bronchial
11	chr1:85853800-85864200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:85854000-85861800	Weak transcription	Osteobl	bone
13	chr1:85854600-85862800	Weak transcription	Liver	Liver
14	chr1:85854600-85863400	Weak transcription	HUVEC	blood vessel
15	chr1:85855200-85870000	Weak transcription	Fetal Stomach	stomach
16	chr1:85856000-85872800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:85858800-85863600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:85859400-85865000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:85860200-85861600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:85860200-85861600	Weak transcription	NH-A	brain
21	chr1:85860200-85862000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr1:85860200-85862800	Weak transcription	NHLF	lung
23	chr1:85860400-85861800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:85860400-85862000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:85860600-85861600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:85860600-85862000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:85860600-85862800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:85861000-85862600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:85861000-85863600	Weak transcription	HSMM	muscle
30	chr1:85861200-85862200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr1:85861200-85862800	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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