Variant report

Variant	rs3816874
Chromosome Location	chr4:20756490-20756491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:20756151..20758021-chr4:20765219..20767901,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10022322	0.83[YRI][hapmap]
rs10031524	0.89[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10084802	0.83[YRI][hapmap]
rs10938801	0.86[YRI][hapmap]
rs10938803	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]
rs11936560	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11940062	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1820505	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1985322	0.83[YRI][hapmap]
rs2114474	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]
rs2288308	0.80[YRI][hapmap]
rs2322687	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2322688	0.83[YRI][hapmap]
rs3764964	0.83[YRI][hapmap]
rs3764965	0.93[YRI][hapmap]
rs4577580	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61428210	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6447971	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6447972	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6447973	0.84[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6447975	0.80[YRI][hapmap]
rs6447978	0.83[YRI][hapmap]
rs6447982	0.91[YRI][hapmap]
rs6811030	0.83[YRI][hapmap]
rs6811933	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6831516	0.83[YRI][hapmap]
rs6857386	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6858843	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7663837	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7668797	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7688592	0.89[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7689421	0.89[CEU][hapmap];0.87[CHB][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7694208	0.89[CEU][hapmap];0.87[CHB][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs964019	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs990206	0.91[YRI][hapmap]

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
rs3816874	C4orf28	Cis_1M	lymphoblastoid	RTeQTL
rs3816874	PACRGL	cis	lung	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20730600-20757600	Weak transcription	HSMM	muscle
2	chr4:20732600-20758400	Weak transcription	Brain Angular Gyrus	brain
3	chr4:20739200-20761200	Weak transcription	Fetal Heart	heart
4	chr4:20740600-20756600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:20740600-20757200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:20740600-20763600	Weak transcription	Brain Anterior Caudate	brain
7	chr4:20740800-20757200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:20740800-20757600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:20740800-20763600	Weak transcription	HSMMtube	muscle
10	chr4:20740800-20770600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:20740800-20791200	Weak transcription	Ovary	ovary
12	chr4:20741000-20757800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:20741800-20757400	Weak transcription	Primary T cells from cord blood	blood
14	chr4:20745600-20757600	Weak transcription	NHEK	skin
15	chr4:20746800-20761400	Weak transcription	Aorta	Aorta
16	chr4:20746800-20775000	Weak transcription	Left Ventricle	heart
17	chr4:20747200-20757600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr4:20747800-20757400	Weak transcription	Fetal Intestine Large	intestine
19	chr4:20749600-20763800	Weak transcription	Brain Germinal Matrix	brain
20	chr4:20751000-20757000	Weak transcription	Primary B cells from cord blood	blood
21	chr4:20753000-20760400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr4:20754200-20757200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:20754400-20756600	Weak transcription	Liver	Liver
24	chr4:20754600-20757000	Weak transcription	NH-A	brain
25	chr4:20754800-20756600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:20754800-20756800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:20754800-20757000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:20755000-20756800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:20755200-20757000	Weak transcription	Adipose Nuclei	Adipose
30	chr4:20755600-20757200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr4:20755800-20761600	Weak transcription	Fetal Lung	lung
32	chr4:20756000-20757600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:20756000-20757600	Weak transcription	Dnd41	blood
34	chr4:20756200-20759200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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