Variant report

Variant	rs11600401
Chromosome Location	chr11:59014969-59014970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11606140	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11607278	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11607673	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12419479	0.81[CEU][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17582175	0.82[CHB][hapmap]
rs2000478	0.92[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2211912	0.88[CEU][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs34697089	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3944255	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4369428	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4939269	0.80[CEU][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5029315	0.89[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs610123	0.92[CEU][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs61903328	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs656163	0.92[CEU][hapmap]
rs6591509	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7113633	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7113936	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7131079	0.84[CEU][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7928981	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7942710	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7944135	0.94[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7944319	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7952377	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3351601	chr11:58979308-59052763	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11600401	DTX4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59012200-59019200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr11:59013200-59015200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr11:59013200-59017000	Enhancers	Primary B cells from cord blood	blood
4	chr11:59013200-59017400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr11:59013400-59016600	Enhancers	Hela-S3	cervix
6	chr11:59014000-59016200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr11:59014200-59015600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr11:59014200-59015800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr11:59014200-59016400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:59014200-59016600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:59014400-59015600	Enhancers	Right Atrium	heart
12	chr11:59014400-59015800	Enhancers	HMEC	breast
13	chr11:59014400-59016000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr11:59014400-59016400	Enhancers	Primary T cells from cord blood	blood
15	chr11:59014400-59016400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:59014400-59016600	Enhancers	Primary T cells fromperipheralblood	blood
17	chr11:59014600-59015000	Enhancers	Lung	lung
18	chr11:59014600-59015200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr11:59014600-59015600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr11:59014600-59015800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:59014600-59015800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr11:59014800-59016000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:59014800-59016400	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links