Variant report

Variant	rs223490
Chromosome Location	chr4:103679117-103679118
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs223331	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs223361	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs223366	0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs223374	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223401	0.82[JPT][hapmap]
rs223413	0.95[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs223471	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs223489	0.95[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008110	chr4:103560583-103684526	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs223490	MANBA	cis	parietal	SCAN
rs223490	MANBA	cis	multi-tissue	Pritchard
rs223490	MANBA	cis	lymphoblastoid	seeQTL
rs223490	KRT8P46	cis	lung	GTEx
rs223490	CISD2	cis	parietal	SCAN
rs223490	ADH7	cis	cerebellum	SCAN
rs223490	LRRC37A15P	cis	Adipose Subcutaneous	GTEx
rs223490	LRRC37A15P	cis	lung	GTEx
rs223490	CISD2	cis	Skin Sun Exposed Lower leg	GTEx
rs223490	CISD2	cis	cerebellum	SCAN
rs223490	MANBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
2	chr4:103637000-103680800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr4:103638800-103681000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:103641200-103680800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:103651000-103681000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:103653000-103680800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:103656000-103680800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:103656400-103680400	Weak transcription	Thymus	Thymus
9	chr4:103656400-103680800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr4:103656400-103680800	Weak transcription	Adipose Nuclei	Adipose
11	chr4:103656600-103680200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:103657000-103680800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:103657400-103680600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:103658000-103680800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:103658600-103681000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr4:103659800-103680800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr4:103661000-103680800	Weak transcription	Fetal Lung	lung
18	chr4:103662000-103680600	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:103662600-103680400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr4:103662800-103680800	Weak transcription	Primary T cells from cord blood	blood
21	chr4:103663400-103681000	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:103664200-103681000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr4:103664200-103681000	Weak transcription	Aorta	Aorta
24	chr4:103665800-103681000	Weak transcription	Fetal Brain Female	brain
25	chr4:103666400-103680400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:103666600-103680800	Weak transcription	NHLF	lung
27	chr4:103667000-103679200	Weak transcription	Dnd41	blood
28	chr4:103667000-103680600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr4:103667800-103680800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr4:103668200-103680600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr4:103668200-103680800	Weak transcription	Brain Angular Gyrus	brain
32	chr4:103668600-103680600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr4:103668600-103680800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:103669400-103680800	Weak transcription	Fetal Brain Male	brain
35	chr4:103669600-103680600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:103670400-103680600	Weak transcription	HSMMtube	muscle
37	chr4:103672800-103680800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:103673600-103680800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:103673800-103681000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:103673800-103681000	Weak transcription	Fetal Thymus	thymus
41	chr4:103675400-103680800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr4:103675600-103680800	Weak transcription	A549	lung
43	chr4:103677800-103680400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr4:103677800-103680400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:103678000-103680400	Enhancers	Fetal Heart	heart
46	chr4:103678000-103680800	Enhancers	Primary B cells from peripheral blood	blood
47	chr4:103678200-103679400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:103678200-103679400	Enhancers	Left Ventricle	heart
49	chr4:103678200-103681000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:103678400-103679200	Enhancers	Hela-S3	cervix

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