Variant report

Variant	rs168248
Chromosome Location	chr3:156547990-156547991
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156537180..156540050-chr3:156547950..156549740,2	K562	blood:
2	chr3:156544049..156546693-chr3:156547441..156549158,2	K562	blood:
3	chr3:156390293..156396385-chr3:156542364..156548172,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197980	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10936040	0.81[YRI][hapmap]
rs11927500	0.88[YRI][hapmap];0.91[AFR][1000 genomes]
rs13321802	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16826858	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs16826899	1.00[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2321290	0.81[YRI][hapmap]
rs2321395	0.89[ASN][1000 genomes]
rs2633815	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs2653817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs344071	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs344072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs344074	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs344076	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs344078	0.96[YRI][hapmap];0.95[AFR][1000 genomes]
rs344083	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs344089	0.91[AFR][1000 genomes]
rs344092	0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs344093	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs414683	0.90[YRI][hapmap];0.91[AFR][1000 genomes]
rs4441614	0.82[AFR][1000 genomes]
rs491423	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55850252	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441099	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6441100	0.95[YRI][hapmap];0.91[AFR][1000 genomes]
rs6441103	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs6763644	1.00[CEU][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6774702	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6786167	1.00[CEU][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6787535	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs6792917	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7630909	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs7635521	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7640994	0.83[AFR][1000 genomes]
rs7650127	0.86[YRI][hapmap]
rs9810194	0.86[AFR][1000 genomes]
rs9841269	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9861359	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs9878709	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs168248	LEKR1	cis	Heart Left Ventricle	GTEx
rs168248	LEKR1	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156545000-156559600	Weak transcription	Pancreas	Pancrea
2	chr3:156545200-156549800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:156545400-156551000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:156545600-156554000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:156545800-156558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:156546000-156549400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:156546000-156549800	Weak transcription	GM12878-XiMat	blood
8	chr3:156546400-156548000	Weak transcription	K562	blood
9	chr3:156547000-156550200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:156547400-156548400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links