Variant report

Variant	rs11841315
Chromosome Location	chr13:48476058-48476059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1104351	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11840968	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12874522	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1326133	0.82[EUR][1000 genomes]
rs1326137	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1359616	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1886977	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2094190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2094195	0.86[EUR][1000 genomes]
rs2094196	1.00[JPT][hapmap]
rs2104481	0.86[EUR][1000 genomes]
rs2182373	0.82[EUR][1000 genomes]
rs2182378	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2406694	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3862747	0.82[EUR][1000 genomes]
rs4941618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs4941624	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4942720	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4942721	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4942724	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4942732	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4942734	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4942736	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4942740	0.82[EUR][1000 genomes]
rs4942746	0.82[EUR][1000 genomes]
rs61972210	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61972223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61972227	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61973264	0.82[EUR][1000 genomes]
rs61973265	0.82[EUR][1000 genomes]
rs61973266	0.82[EUR][1000 genomes]
rs61974562	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61974563	0.82[EUR][1000 genomes]
rs61974564	0.82[EUR][1000 genomes]
rs61974579	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6561414	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6561416	0.82[EUR][1000 genomes]
rs6561421	0.82[EUR][1000 genomes]
rs6561425	0.82[EUR][1000 genomes]
rs6561426	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7323702	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs7323821	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7324368	0.80[EUR][1000 genomes]
rs7325175	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7326418	0.82[EUR][1000 genomes]
rs7329137	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7329266	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7329615	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7332363	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs7332994	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs7335797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs753372	1.00[JPT][hapmap]
rs7990099	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs7990541	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7991892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs7996051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7996581	0.85[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs7998786	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8001032	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8001509	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8002482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8002847	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs840428	0.82[EUR][1000 genomes]
rs840429	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs840432	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs840435	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs840437	0.82[EUR][1000 genomes]
rs840439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs943066	0.82[EUR][1000 genomes]
rs943067	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9526419	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9526431	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9534884	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9534934	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9562792	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9567927	1.00[JPT][hapmap]
rs9567988	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][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	esv3510679	chr13:48236624-48498185	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3510680	chr13:48236624-48498185	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	esv1803690	chr13:48470681-48508091	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11841315	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs11841315	SUCLA2	cis	multi-tissue	Pritchard
rs11841315	MED4	cis	normal skin	skin_eQTL
rs11841315	MED4	cis	lesional skin	skin_eQTL
rs11841315	MED4	cis	uninvolved skin	skin_eQTL
rs11841315	MED4	cis	multi-tissue	Pritchard

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48451000-48480200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr13:48457200-48478000	Weak transcription	Adipose Nuclei	Adipose
3	chr13:48461000-48478200	Weak transcription	Left Ventricle	heart
4	chr13:48465000-48484000	Weak transcription	Primary T cells from cord blood	blood
5	chr13:48465200-48478200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:48468600-48485600	Weak transcription	Gastric	stomach
7	chr13:48468800-48479600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr13:48468800-48482400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr13:48469000-48478200	Weak transcription	Esophagus	oesophagus
10	chr13:48470400-48478000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:48472000-48477800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:48472000-48482200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:48472200-48482400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr13:48472200-48482400	Weak transcription	NHEK	skin
15	chr13:48472200-48491400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr13:48475600-48476200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:48475600-48476400	Enhancers	NH-A	brain
18	chr13:48475800-48476200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr13:48475800-48476600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr13:48476000-48478000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:48476000-48479800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links