Variant report

Variant	rs344088
Chromosome Location	chr3:156561361-156561362
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	chr3:156559469..156561892-chr3:156564883..156566469,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11710516	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11717138	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11927500	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13321802	1.00[JPT][hapmap]
rs1430412	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16826858	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16826864	0.89[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16826899	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16826906	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16826948	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs171077	0.83[ASN][1000 genomes]
rs171080	0.89[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs180746	0.83[ASN][1000 genomes]
rs182936	0.83[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs237246	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2633815	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2653817	0.87[GIH][hapmap]
rs28661978	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2874490	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2874491	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs343992	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs344023	0.83[ASN][1000 genomes]
rs344047	0.83[ASN][1000 genomes]
rs344048	0.83[ASN][1000 genomes]
rs344049	0.83[ASN][1000 genomes]
rs344050	0.83[ASN][1000 genomes]
rs344063	1.00[JPT][hapmap]
rs344076	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344077	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344078	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344081	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344083	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs344085	0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344086	0.89[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344089	0.90[ASN][1000 genomes]
rs344090	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344091	0.89[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs344092	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs344093	0.83[ASN][1000 genomes]
rs3796172	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs414683	1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4441614	0.84[ASN][1000 genomes]
rs4680298	0.83[CHD][hapmap]
rs4680299	0.83[CHD][hapmap]
rs4680304	0.84[ASN][1000 genomes]
rs491423	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55850252	0.84[ASN][1000 genomes]
rs58207863	0.84[ASN][1000 genomes]
rs59244547	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441092	0.83[CHD][hapmap]
rs6441099	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6441100	0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6441103	0.97[GIH][hapmap];0.89[ASN][1000 genomes]
rs6441104	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6763233	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6763644	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6774702	0.84[ASN][1000 genomes]
rs6786167	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6787535	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6787952	0.89[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6792917	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs6795327	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6795516	0.88[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6799457	0.83[CHD][hapmap]
rs6802042	1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6802511	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs7426821	0.84[ASN][1000 genomes]
rs7609851	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.82[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7616633	0.81[GIH][hapmap]
rs7618306	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7621699	0.89[CEU][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7630909	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7635521	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7640994	0.89[ASN][1000 genomes]
rs7650127	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs978108	0.83[CHD][hapmap]
rs9810194	0.84[ASN][1000 genomes]
rs9841269	0.84[ASN][1000 genomes]
rs9847692	1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9861359	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9878709	1.00[JPT][hapmap];0.95[ASN][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	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs344088	LEKR1	cis	parietal	SCAN
rs344088	IKBKE	trans	parietal	SCAN
rs344088	LEKR1	cis	cerebellum	SCAN
rs344088	SLC23A3	trans	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156559400-156561600	Enhancers	Fetal Brain Male	brain
2	chr3:156560800-156561600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr3:156561000-156561400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:156561000-156561400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:156561000-156561600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:156561000-156561600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:156561000-156561600	Active TSS	Aorta	Aorta
8	chr3:156561000-156561600	Active TSS	NHDF-Ad	bronchial
9	chr3:156561000-156561600	Active TSS	Osteobl	bone
10	chr3:156561000-156561800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:156561200-156561400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:156561200-156561600	Enhancers	Liver	Liver
13	chr3:156561200-156562800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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