Variant report

Variant	rs11727546
Chromosome Location	chr4:103557664-103557665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1054029	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap]
rs1054037	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs1077358	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs11724614	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs12498722	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12644381	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs13106304	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs13106325	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs17033015	0.91[JPT][hapmap]
rs179195	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2125211	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2272695	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2272696	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2272697	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs227276	0.82[CHB][hapmap]
rs227277	0.82[CHB][hapmap]
rs227361	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs228611	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs228614	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs228617	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs228618	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs228619	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs228623	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs2866407	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2866412	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2866413	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs2866414	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs2903283	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3733202	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3774968	0.83[JPT][hapmap]
rs4013	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs404574	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap]
rs434644	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4496586	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs4547797	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs4586937	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs5026472	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs5026473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs5026474	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs5026476	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs6533020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs6533021	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs6810869	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs6812747	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs6839064	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs735403	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs735404	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs735405	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs7674640	0.88[CEU][hapmap];0.85[CHB][hapmap]
rs7677509	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7699231	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7699678	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs909349	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003618	chr4:103530465-103562161	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1799158	chr4:103556316-103580296	Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11727546	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103536200-103595400	Weak transcription	Colonic Mucosa	Colon
2	chr4:103536600-103562600	Weak transcription	Brain Germinal Matrix	brain
3	chr4:103536600-103595800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:103541800-103562400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:103541800-103571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr4:103542400-103560800	Weak transcription	Brain Substantia Nigra	brain
7	chr4:103542400-103562200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr4:103542400-103578800	Weak transcription	Psoas Muscle	Psoas
9	chr4:103542400-103594400	Weak transcription	K562	blood
10	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:103542800-103563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:103545200-103559800	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:103545200-103592000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
15	chr4:103549000-103570400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:103549600-103558600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:103549600-103561600	Weak transcription	NHDF-Ad	bronchial
18	chr4:103549800-103561600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr4:103549800-103561600	Weak transcription	Osteobl	bone
20	chr4:103549800-103572000	Weak transcription	Placenta	Placenta
21	chr4:103550200-103582800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:103550400-103573000	Weak transcription	Fetal Kidney	kidney
23	chr4:103551000-103562600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:103551000-103563000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:103551000-103565000	Strong transcription	Primary B cells from cord blood	blood
26	chr4:103551000-103607600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr4:103551000-103607800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr4:103551600-103564000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:103551800-103563200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:103552000-103561000	Strong transcription	Stomach Smooth Muscle	stomach
31	chr4:103552000-103562800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr4:103552000-103563400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr4:103552400-103559200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:103552400-103560800	Strong transcription	Primary hematopoietic stem cells	blood
35	chr4:103552400-103561200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr4:103552400-103561600	Weak transcription	NHEK	skin
37	chr4:103552400-103579600	Weak transcription	Fetal Heart	heart
38	chr4:103552800-103558600	Strong transcription	Adipose Nuclei	Adipose
39	chr4:103552800-103558800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr4:103552800-103561000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr4:103552800-103561000	Strong transcription	Left Ventricle	heart
42	chr4:103552800-103561200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:103552800-103561200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr4:103552800-103561800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr4:103553000-103651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:103553200-103558400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:103553200-103591200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr4:103553400-103559200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr4:103553400-103567800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:103553400-103568000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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