Variant report

Variant	rs554215
Chromosome Location	chr3:101029237-101029238
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	chr3:101020011..101022756-chr3:101027193..101029780,2	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10451923	0.82[ASN][1000 genomes]
rs10511189	0.89[ASN][1000 genomes]
rs11918335	0.82[EUR][1000 genomes]
rs11919906	0.86[EUR][1000 genomes]
rs12636505	0.82[EUR][1000 genomes]
rs13347262	0.82[EUR][1000 genomes]
rs1405781	0.82[EUR][1000 genomes]
rs1520654	0.93[ASN][1000 genomes]
rs16843627	0.93[ASN][1000 genomes]
rs16843634	0.94[ASN][1000 genomes]
rs16843699	0.97[ASN][1000 genomes]
rs16843817	0.80[ASN][1000 genomes]
rs17487	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1880982	0.82[EUR][1000 genomes]
rs1986294	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271972	0.93[ASN][1000 genomes]
rs2449822	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2460724	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35902489	0.91[ASN][1000 genomes]
rs3732893	0.88[ASN][1000 genomes]
rs3773915	1.00[ASN][1000 genomes]
rs3773917	0.94[ASN][1000 genomes]
rs3773918	0.94[ASN][1000 genomes]
rs4553955	0.82[ASN][1000 genomes]
rs475521	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs476090	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs476491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478173	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs479522	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs479723	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481809	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs482055	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs482436	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs482976	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs483947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs485130	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs489455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500480	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs501702	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505037	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs512242	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs512357	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs513188	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513994	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs515307	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs516312	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517698	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs522749	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs527836	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs530566	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs535881	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs536561	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs538834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs545322	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546090	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550241	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs559042	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs559400	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs563909	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs567983	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs569339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs570318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571883	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs573908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62280636	0.87[ASN][1000 genomes]
rs62280637	0.84[ASN][1000 genomes]
rs62280663	0.82[ASN][1000 genomes]
rs62280664	0.82[ASN][1000 genomes]
rs62280670	0.80[ASN][1000 genomes]
rs62280671	0.82[ASN][1000 genomes]
rs62280673	0.82[ASN][1000 genomes]
rs62280674	0.82[ASN][1000 genomes]
rs62280675	0.82[ASN][1000 genomes]
rs62280746	0.86[EUR][1000 genomes]
rs62282871	0.91[ASN][1000 genomes]
rs62282873	0.91[ASN][1000 genomes]
rs62282875	0.93[ASN][1000 genomes]
rs62282885	0.94[ASN][1000 genomes]
rs62282886	0.97[ASN][1000 genomes]
rs62282887	1.00[ASN][1000 genomes]
rs62282888	1.00[ASN][1000 genomes]
rs62282889	1.00[ASN][1000 genomes]
rs62282890	0.92[ASN][1000 genomes]
rs62282892	0.82[ASN][1000 genomes]
rs6441595	0.94[ASN][1000 genomes]
rs6777720	0.82[EUR][1000 genomes]
rs6796058	0.84[ASN][1000 genomes]
rs6798685	0.84[ASN][1000 genomes]
rs693428	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72932462	0.91[ASN][1000 genomes]
rs7611378	0.94[ASN][1000 genomes]
rs7621506	0.82[ASN][1000 genomes]
rs7632064	0.93[ASN][1000 genomes]
rs7634592	0.93[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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv877222	chr3:100715576-101038297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101026600-101029400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:101028000-101044200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:101028400-101030800	Enhancers	Fetal Kidney	kidney
4	chr3:101028800-101029600	Weak transcription	HUVEC	blood vessel
5	chr3:101028800-101030200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr3:101028800-101031000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:101028800-101032800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:101029000-101029400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:101029000-101029400	Enhancers	Ovary	ovary
10	chr3:101029000-101029400	Enhancers	Osteobl	bone
11	chr3:101029000-101029800	Strong transcription	Primary T cells from cord blood	blood
12	chr3:101029000-101030200	Enhancers	Fetal Stomach	stomach
13	chr3:101029000-101030800	Enhancers	Colon Smooth Muscle	Colon
14	chr3:101029000-101030800	Enhancers	Rectal Smooth Muscle	rectum
15	chr3:101029200-101029600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:101029200-101029600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:101029200-101029800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:101029200-101030200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:101029200-101030200	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links