Variant report

Variant	rs974726
Chromosome Location	chr4:20702506-20702507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:20700245..20702604-chr4:20707211..20709448,2	MCF-7	breast:
2	chr4:20702290..20703806-chr4:20728599..20731005,2	K562	blood:
3	chr4:20702272..20703966-chr4:20709575..20711144,2	MCF-7	breast:
4	chr4:20700439..20703043-chr4:20709421..20711457,2	MCF-7	breast:
5	chr4:20702290..20704847-chr4:20728043..20731005,3	K562	blood:
6	chr4:20693086..20698959-chr4:20699230..20704175,9	K562	blood:

Variant related genes	Relation type
ENSG00000163138	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10755201	0.81[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13149547	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1426883	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17623902	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1896192	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1902848	0.83[AFR][1000 genomes]
rs2322639	0.82[AFR][1000 genomes]
rs2874830	0.83[AFR][1000 genomes]
rs3911552	0.82[AFR][1000 genomes]
rs4696963	0.83[AFR][1000 genomes]
rs4697177	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7697118	0.83[AFR][1000 genomes]
rs967942	0.82[AFR][1000 genomes]
rs991173	0.82[AFR][1000 genomes]
rs9991750	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[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	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers 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	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs974726	PACRGL	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20701000-20702800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:20701000-20703200	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr4:20701000-20703400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:20701200-20702600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:20701200-20702600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:20701200-20702600	Active TSS	Brain Substantia Nigra	brain
7	chr4:20701200-20702800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr4:20701200-20702800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:20701200-20702800	Active TSS	Fetal Muscle Trunk	muscle
10	chr4:20701200-20702800	Active TSS	Rectal Smooth Muscle	rectum
11	chr4:20701200-20702800	Active TSS	Right Atrium	heart
12	chr4:20701200-20703000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr4:20701200-20703000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:20701200-20703000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr4:20701200-20703000	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr4:20701200-20703000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:20701200-20703000	Active TSS	Fetal Kidney	kidney
18	chr4:20701200-20703200	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr4:20701200-20703200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr4:20701200-20703200	Active TSS	Right Ventricle	heart
21	chr4:20701200-20703400	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr4:20701400-20702600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr4:20701400-20702600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr4:20701400-20702600	Active TSS	Brain Angular Gyrus	brain
25	chr4:20701400-20702600	Active TSS	Brain Germinal Matrix	brain
26	chr4:20701400-20702600	Active TSS	Brain Hippocampus Middle	brain
27	chr4:20701400-20702600	Active TSS	Colon Smooth Muscle	Colon
28	chr4:20701400-20702600	Active TSS	Fetal Brain Male	brain
29	chr4:20701400-20702600	Active TSS	Fetal Intestine Large	intestine
30	chr4:20701400-20702600	Active TSS	Fetal Lung	lung
31	chr4:20701400-20702600	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr4:20701400-20702800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:20701400-20702800	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr4:20701400-20702800	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr4:20701400-20702800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:20701400-20702800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr4:20701400-20702800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:20701400-20702800	Active TSS	Aorta	Aorta
39	chr4:20701400-20702800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr4:20701400-20702800	Active TSS	Fetal Intestine Small	intestine
41	chr4:20701400-20702800	Active TSS	Fetal Muscle Leg	muscle
42	chr4:20701400-20702800	Active TSS	Ovary	ovary
43	chr4:20701400-20702800	Active TSS	NHDF-Ad	bronchial
44	chr4:20701400-20703000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr4:20701400-20703000	Active TSS	Left Ventricle	heart
46	chr4:20701400-20703000	Active TSS	HSMMtube	muscle
47	chr4:20701400-20703200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr4:20701400-20703200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:20701400-20703200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:20701400-20703200	Active TSS	Pancreatic Islets	Pancreatic Islet

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