Variant report

Variant	rs2114474
Chromosome Location	chr4:20733270-20733271
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10031524	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10938803	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]
rs11936560	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11940062	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1820505	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2322687	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3764965	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs3816874	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4577580	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61428210	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6447971	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6447972	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6447973	0.88[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6811933	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6857386	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6858843	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7663837	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7668797	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7688592	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7689421	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7694208	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs964019	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2114474	C4orf28	Cis_1M	lymphoblastoid	RTeQTL
rs2114474	PACRGL	cis	Thyroid	GTEx
rs2114474	PACRGL	cis	lung	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20703000-20741400	Weak transcription	Stomach Mucosa	stomach
2	chr4:20703200-20741000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:20706800-20738600	Weak transcription	Psoas Muscle	Psoas
4	chr4:20707200-20739400	Weak transcription	HepG2	liver
5	chr4:20708200-20733600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:20715400-20738600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:20715400-20739400	Weak transcription	Osteobl	bone
8	chr4:20718000-20738600	Weak transcription	NHDF-Ad	bronchial
9	chr4:20718200-20738400	Weak transcription	Fetal Heart	heart
10	chr4:20721800-20736000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:20721800-20736400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:20721800-20737200	Strong transcription	Liver	Liver
13	chr4:20722800-20735800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:20723000-20738400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:20724200-20736000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr4:20724200-20736000	Strong transcription	Adipose Nuclei	Adipose
17	chr4:20724200-20737000	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr4:20724200-20738800	Weak transcription	Gastric	stomach
19	chr4:20724200-20738800	Weak transcription	Small Intestine	intestine
20	chr4:20724400-20735200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr4:20724400-20735400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:20724400-20735400	Weak transcription	Lung	lung
23	chr4:20724400-20735400	Weak transcription	Pancreas	Pancrea
24	chr4:20724400-20735600	Strong transcription	Dnd41	blood
25	chr4:20724400-20735800	Strong transcription	Fetal Intestine Large	intestine
26	chr4:20724400-20736200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:20724400-20736200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:20724400-20737000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:20724400-20737000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:20724400-20738400	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr4:20724400-20738800	Weak transcription	Esophagus	oesophagus
32	chr4:20724400-20738800	Weak transcription	HMEC	breast
33	chr4:20724400-20739000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr4:20724400-20739400	Weak transcription	Fetal Thymus	thymus
35	chr4:20724400-20739400	Weak transcription	Thymus	Thymus
36	chr4:20724400-20739400	Weak transcription	Spleen	Spleen
37	chr4:20724400-20740000	Weak transcription	GM12878-XiMat	blood
38	chr4:20724600-20739200	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr4:20724600-20742000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:20724800-20735400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:20724800-20735400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr4:20724800-20736800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:20724800-20738600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:20724800-20738600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:20724800-20738600	Weak transcription	Fetal Brain Male	brain
46	chr4:20724800-20738800	Weak transcription	Brain Substantia Nigra	brain
47	chr4:20724800-20741600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:20725000-20733600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:20725000-20738200	Weak transcription	NHEK	skin
50	chr4:20725000-20738400	Weak transcription	A549	lung

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