Variant report

Variant	rs189236
Chromosome Location	chr4:130028412-130028413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10028974	0.96[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs11098994	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes]
rs12500557	0.85[YRI][hapmap]
rs1376202	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap]
rs172168	0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1756011	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1757926	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757929	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1757937	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1757938	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1757942	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1838911	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2118045	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2592948	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2597837	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2655311	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2777822	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2777823	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs280594	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs280596	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs280597	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs280601	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs3099902	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3099903	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3113487	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3113488	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs337276	0.84[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs337279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530686	0.85[ASN][1000 genomes]
rs62316971	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62316978	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7654405	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs796886	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	79 gene(s)	inside rSNPs	diseases
2	nsv534538	chr4:129799138-130431688	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv879931	chr4:129939775-130178102	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs189236	LOC132321	cis	normal skin	skin_eQTL
rs189236	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs189236	C4orf33	cis	Artery Tibial	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:130017600-130031400	Weak transcription	Pancreas	Pancrea
2	chr4:130017600-130031400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:130017600-130040400	Weak transcription	Lung	lung
4	chr4:130017800-130030800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:130017800-130031400	Weak transcription	Aorta	Aorta
6	chr4:130017800-130031400	Weak transcription	Left Ventricle	heart
7	chr4:130017800-130031400	Weak transcription	Ovary	ovary
8	chr4:130017800-130031400	Weak transcription	Right Ventricle	heart
9	chr4:130017800-130031600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr4:130017800-130032600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr4:130017800-130032800	Weak transcription	Colon Smooth Muscle	Colon
12	chr4:130017800-130033400	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:130017800-130033400	Weak transcription	Thymus	Thymus
14	chr4:130017800-130034200	Weak transcription	Colonic Mucosa	Colon
15	chr4:130018000-130030200	Weak transcription	Primary T cells from cord blood	blood
16	chr4:130018000-130030400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr4:130018000-130030600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:130018000-130031000	Weak transcription	Fetal Thymus	thymus
19	chr4:130018000-130031400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr4:130018000-130031400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:130018000-130031400	Weak transcription	Fetal Stomach	stomach
22	chr4:130018000-130032400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:130018000-130033000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:130018000-130033200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:130018000-130033400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr4:130018000-130034000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:130018000-130038000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr4:130018200-130030600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:130018200-130031800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:130018200-130032400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:130018600-130032000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:130018800-130033800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:130020200-130030400	Weak transcription	K562	blood
34	chr4:130020600-130030200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr4:130023600-130033400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr4:130024200-130030600	Weak transcription	Fetal Heart	heart
37	chr4:130025000-130030000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:130025000-130032000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:130025200-130033200	Weak transcription	Fetal Lung	lung
40	chr4:130025400-130030200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:130025400-130032200	Weak transcription	Fetal Brain Male	brain
42	chr4:130025600-130030400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:130025800-130030200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr4:130025800-130030400	Weak transcription	Adipose Nuclei	Adipose
45	chr4:130025800-130030600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:130025800-130030600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr4:130025800-130035000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr4:130026000-130030200	Weak transcription	Primary B cells from cord blood	blood
49	chr4:130026000-130030200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:130026000-130030400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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