Variant report

Variant	rs990916
Chromosome Location	chr1:85898508-85898509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1006989	0.84[CEU][hapmap];0.89[EUR][1000 genomes]
rs10489510	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10747318	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10782549	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10873701	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10873702	0.88[CEU][hapmap]
rs10873703	0.81[JPT][hapmap]
rs1146378	0.82[ASN][1000 genomes]
rs1146383	0.87[JPT][hapmap]
rs12022248	0.93[ASN][1000 genomes]
rs12029221	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12032315	0.82[ASN][1000 genomes]
rs12033483	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12034249	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12035116	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12038426	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042780	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12047189	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1261681	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1342323	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1357635	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1357636	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1391556	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1523994	0.89[CEU][hapmap]
rs1523995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1608537	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17384213	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17388696	0.93[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965876	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1975755	0.89[CEU][hapmap]
rs2016104	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037594	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs2064510	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124139	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124140	0.86[ASN][1000 genomes]
rs2300633	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2389948	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851268	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4428939	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4512701	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4631749	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4949889	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4949897	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4949898	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4949899	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs499869	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs539714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600098	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs604974	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs631817	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6420965	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs659070	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6672870	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72722663	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72722671	0.86[ASN][1000 genomes]
rs72722691	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72722692	0.94[AMR][1000 genomes]
rs72724608	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs731194	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7515261	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7539738	0.89[EUR][1000 genomes]
rs7555670	0.84[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85874000-85903800	Weak transcription	NHLF	lung
2	chr1:85874200-85903600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:85874400-85903600	Weak transcription	HepG2	liver
4	chr1:85874400-85904200	Weak transcription	NH-A	brain
5	chr1:85886400-85899000	Weak transcription	NHDF-Ad	bronchial
6	chr1:85886400-85903800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:85886400-85914200	Weak transcription	HSMMtube	muscle
8	chr1:85886800-85903800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:85887600-85902200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:85887600-85903400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:85890400-85902200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:85892200-85906200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:85893800-85906200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr1:85893800-85916800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:85894400-85903600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:85894600-85903600	Weak transcription	Adipose Nuclei	Adipose
17	chr1:85894600-85903800	Weak transcription	HUVEC	blood vessel
18	chr1:85894600-85904200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:85896400-85899400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:85897000-85899200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:85897000-85899400	Strong transcription	HSMM	muscle
22	chr1:85897000-85904200	Weak transcription	Fetal Intestine Large	intestine
23	chr1:85897200-85899200	Strong transcription	Osteobl	bone
24	chr1:85897400-85900400	Weak transcription	Fetal Brain Female	brain
25	chr1:85897800-85904200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:85897800-85904800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:85898000-85902200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:85898200-85903600	Weak transcription	Liver	Liver

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