Variant report

Variant	rs1048696
Chromosome Location	chr11:58976634-58976635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10501375	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10501376	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896949	0.80[EUR][1000 genomes]
rs10896950	0.80[EUR][1000 genomes]
rs10896957	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11229868	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11229869	1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229870	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229872	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229873	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229874	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229875	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229882	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11229889	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs11229901	0.90[EUR][1000 genomes]
rs11229902	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes]
rs11229903	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs11229904	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes]
rs12223401	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12284370	0.80[EUR][1000 genomes]
rs12575770	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12576150	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12576412	1.00[CEU][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12576558	0.85[EUR][1000 genomes]
rs12576879	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12577252	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17153538	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1938595	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35654554	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3740946	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3781796	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59466005	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60265864	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61086875	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7104296	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7104437	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7926933	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7942203	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869155	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1048696	DTX4	Cis_1M	lymphoblastoid	RTeQTL
rs1048696	MPEG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:58956400-58977400	Weak transcription	Hela-S3	cervix
3	chr11:58964400-58977400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:58965800-58978000	Weak transcription	Left Ventricle	heart
5	chr11:58972000-58977600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
6	chr11:58973400-58978200	Weak transcription	Esophagus	oesophagus
7	chr11:58973400-58983200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:58973600-58977000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:58973600-58977200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:58973600-58982000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:58973800-58977400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr11:58973800-58979600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:58973800-58984000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:58974200-58976800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:58974400-58977200	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
16	chr11:58974600-58976800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:58974600-58977000	Weak transcription	Fetal Kidney	kidney
18	chr11:58974600-58978600	Weak transcription	Pancreas	Pancrea
19	chr11:58974600-58978800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:58974800-58976800	Flanking Active TSS	GM12878-XiMat	blood
21	chr11:58974800-58977400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:58974800-58977800	Weak transcription	Colonic Mucosa	Colon
23	chr11:58974800-58980200	Weak transcription	Brain Germinal Matrix	brain
24	chr11:58975000-58980400	Weak transcription	Fetal Brain Female	brain
25	chr11:58975200-58976800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr11:58975200-58976800	Genic enhancers	Fetal Stomach	stomach
27	chr11:58975200-58977000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:58975200-58977800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr11:58975200-58980000	Weak transcription	Lung	lung
30	chr11:58975400-58980000	Active TSS	Duodenum Mucosa	Duodenum
31	chr11:58975400-58986600	Weak transcription	Gastric	stomach
32	chr11:58975600-58976800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr11:58975600-58977000	Enhancers	Osteobl	bone
34	chr11:58975600-58977400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:58975600-58977400	Enhancers	HSMMtube	muscle
36	chr11:58975600-58977600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr11:58975600-58978200	Enhancers	Fetal Brain Male	brain
38	chr11:58975600-58978200	Weak transcription	Small Intestine	intestine
39	chr11:58975600-58978800	Weak transcription	Brain Substantia Nigra	brain
40	chr11:58975600-58980200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:58975800-58977000	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr11:58975800-58977800	Weak transcription	Fetal Intestine Small	intestine
43	chr11:58975800-58978000	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:58975800-58978400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:58975800-58978400	Weak transcription	Brain Anterior Caudate	brain
46	chr11:58975800-58980000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:58975800-58980400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:58975800-58980400	Active TSS	Fetal Intestine Large	intestine
49	chr11:58975800-58980800	Active TSS	Adipose Nuclei	Adipose
50	chr11:58975800-58981800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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