Variant report

Variant	rs10938803
Chromosome Location	chr4:20749299-20749300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10031524	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11936560	0.88[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11940062	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1820505	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2114474	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[LWK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2322687	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3764965	0.88[CEU][hapmap]
rs3816874	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4577580	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61428210	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6447971	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6447972	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6447973	0.82[ASW][hapmap];0.96[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811933	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6857386	1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6858843	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7663837	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7668797	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7688592	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7689421	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7694208	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs964019	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][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	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv869522	chr4:20724433-20938248	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10938803	C4orf28	Cis_1M	lymphoblastoid	RTeQTL
rs10938803	PACRGL	cis	lung	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20725000-20753000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:20730600-20757600	Weak transcription	HSMM	muscle
3	chr4:20732600-20758400	Weak transcription	Brain Angular Gyrus	brain
4	chr4:20739200-20761200	Weak transcription	Fetal Heart	heart
5	chr4:20739600-20755200	Weak transcription	K562	blood
6	chr4:20740200-20755200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:20740600-20754800	Weak transcription	Dnd41	blood
8	chr4:20740600-20756600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:20740600-20757200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:20740600-20763600	Weak transcription	Brain Anterior Caudate	brain
11	chr4:20740800-20750800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:20740800-20751400	Weak transcription	Pancreas	Pancrea
13	chr4:20740800-20756000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:20740800-20757200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:20740800-20757600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:20740800-20763600	Weak transcription	HSMMtube	muscle
17	chr4:20740800-20770600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr4:20740800-20791200	Weak transcription	Ovary	ovary
19	chr4:20741000-20753600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:20741000-20757800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:20741600-20754200	Weak transcription	Fetal Lung	lung
22	chr4:20741600-20756200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:20741800-20757400	Weak transcription	Primary T cells from cord blood	blood
24	chr4:20745600-20757600	Weak transcription	NHEK	skin
25	chr4:20746800-20761400	Weak transcription	Aorta	Aorta
26	chr4:20746800-20775000	Weak transcription	Left Ventricle	heart
27	chr4:20747200-20754800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:20747200-20757600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:20747400-20755400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:20747400-20755800	Weak transcription	Fetal Brain Female	brain
31	chr4:20747600-20754200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:20747600-20754600	Weak transcription	Fetal Muscle Leg	muscle
33	chr4:20747600-20755800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:20747800-20753400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:20747800-20753400	Weak transcription	Adipose Nuclei	Adipose
36	chr4:20747800-20754200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:20747800-20757400	Weak transcription	Fetal Intestine Large	intestine
38	chr4:20748000-20756200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr4:20748200-20754000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:20749000-20749600	Strong transcription	Brain Germinal Matrix	brain
41	chr4:20749200-20749600	Strong transcription	Fetal Stomach	stomach
42	chr4:20749200-20750000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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