Variant report

Variant	rs4939260
Chromosome Location	chr11:58982694-58982695
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1048444	0.96[CEU][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10792228	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10896953	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10896956	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10896958	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11229896	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11229898	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11229899	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11600294	0.85[AMR][1000 genomes]
rs12280107	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17153461	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1938593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1945592	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1945593	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2000875	0.96[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3847	0.96[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4938915	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4939263	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4939267	0.96[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5023474	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5023475	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61689139	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6591510	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6591515	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6591517	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7109866	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111287	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7113607	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7121247	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7129035	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129362	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7931234	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7938115	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	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
6	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4939260	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs4939260	MPEG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58973400-58983200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:58973800-58984000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:58975400-58986600	Weak transcription	Gastric	stomach
4	chr11:58976000-58989400	Weak transcription	Stomach Mucosa	stomach
5	chr11:58977600-58984000	Weak transcription	Fetal Lung	lung
6	chr11:58978600-58984000	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:58979200-58989600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr11:58979400-58983800	Weak transcription	Fetal Stomach	stomach
9	chr11:58979800-58985200	Weak transcription	Pancreas	Pancrea
10	chr11:58980000-58984200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr11:58980400-58984200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:58980400-58984200	Weak transcription	Fetal Thymus	thymus
13	chr11:58980400-58984400	Weak transcription	Fetal Intestine Small	intestine
14	chr11:58980400-58991200	Weak transcription	Fetal Muscle Leg	muscle
15	chr11:58980800-58983200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr11:58981000-58982800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr11:58981000-58983000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr11:58981000-58983000	Weak transcription	Placenta	Placenta
19	chr11:58981000-58984000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr11:58981000-58984000	Enhancers	Primary B cells from cord blood	blood
21	chr11:58981000-58984200	Enhancers	Primary B cells from peripheral blood	blood
22	chr11:58981000-58984200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr11:58981000-58991600	Weak transcription	Spleen	Spleen
24	chr11:58981200-58983600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:58981200-58984000	Weak transcription	Adipose Nuclei	Adipose
26	chr11:58981600-58983600	Enhancers	GM12878-XiMat	blood
27	chr11:58982400-58983600	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr11:58982600-58983000	Enhancers	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links