Variant report

Variant	rs1990524
Chromosome Location	chr4:15420833-15420834
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10002931	0.84[EUR][1000 genomes]
rs10003338	0.85[EUR][1000 genomes]
rs10032941	0.82[EUR][1000 genomes]
rs10212844	0.84[EUR][1000 genomes]
rs10212901	0.83[EUR][1000 genomes]
rs10213628	0.84[EUR][1000 genomes]
rs1024758	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1024759	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10461112	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10488970	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11934015	0.84[EUR][1000 genomes]
rs11937671	0.84[EUR][1000 genomes]
rs12233742	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13104095	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13106702	0.85[EUR][1000 genomes]
rs13114788	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13116208	0.81[CHD][hapmap]
rs13120744	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13123050	0.90[ASN][1000 genomes]
rs13123785	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13124324	0.84[EUR][1000 genomes]
rs13124984	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129124	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13132007	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13132446	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13132604	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138481	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138554	0.88[ASN][1000 genomes]
rs16891929	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891934	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891939	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16891945	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17469724	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2192355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192356	0.86[CHD][hapmap]
rs2192364	0.84[EUR][1000 genomes]
rs28376639	0.84[EUR][1000 genomes]
rs28561808	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2872704	0.84[EUR][1000 genomes]
rs34028526	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34351987	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34352292	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34400909	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34496443	0.90[ASN][1000 genomes]
rs35301498	0.90[ASN][1000 genomes]
rs35465107	0.88[ASN][1000 genomes]
rs35539860	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35866305	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35971217	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797006	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3822296	0.83[EUR][1000 genomes]
rs58479200	0.90[ASN][1000 genomes]
rs59684117	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61240629	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62289285	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449138	0.84[EUR][1000 genomes]
rs66696244	0.89[ASN][1000 genomes]
rs67391897	0.90[ASN][1000 genomes]
rs68012715	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6828721	0.84[EUR][1000 genomes]
rs6855244	0.84[EUR][1000 genomes]
rs71601473	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71601477	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs722235	0.88[ASN][1000 genomes]
rs7442554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681816	0.84[EUR][1000 genomes]
rs7687272	0.84[EUR][1000 genomes]
rs7690471	0.84[EUR][1000 genomes]
rs7697778	0.84[EUR][1000 genomes]
rs9991652	0.84[EUR][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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1990524	HS3ST1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15405400-15422000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr4:15412400-15421800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:15412600-15421800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr4:15416800-15421800	Weak transcription	NHLF	lung
5	chr4:15416800-15422000	Weak transcription	Brain Substantia Nigra	brain
6	chr4:15416800-15422000	Weak transcription	HSMMtube	muscle
7	chr4:15416800-15422000	Weak transcription	NH-A	brain
8	chr4:15416800-15429000	Weak transcription	Fetal Lung	lung
9	chr4:15417000-15421800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:15417000-15421800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:15417000-15421800	Weak transcription	HSMM	muscle
12	chr4:15417000-15421800	Weak transcription	Osteobl	bone
13	chr4:15418000-15423200	Enhancers	Ovary	ovary
14	chr4:15418200-15423200	Enhancers	Colon Smooth Muscle	Colon
15	chr4:15418400-15422600	Weak transcription	Right Atrium	heart
16	chr4:15418600-15421600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:15419000-15422000	Enhancers	Aorta	Aorta
18	chr4:15419000-15428600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:15419400-15421800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:15419800-15428600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr4:15420000-15422800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:15420600-15421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:15420800-15421000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:15420800-15421600	Enhancers	Stomach Smooth Muscle	stomach
25	chr4:15420800-15428800	Weak transcription	Fetal Stomach	stomach

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