Variant report

Variant	rs9851992
Chromosome Location	chr3:61545021-61545022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:61544960-61545110	HRE	kidney:	n/a	n/a
2	CTCF	chr3:61544774-61545076	GM12878	blood:	n/a	n/a
3	RAD21	chr3:61544798-61545060	SK-N-SH_RA	brain:	n/a	n/a
4	CTCF	chr3:61544900-61545050	NHLF	lung:	n/a	n/a
5	CTCF	chr3:61544900-61545050	AG04450	lung:	n/a	n/a
6	CTCF	chr3:61544796-61545098	IMR90	lung:	n/a	n/a
7	MAFK	chr3:61545020-61545220	H1-hESC	embryonic stem cell:	n/a	n/a
8	CTCF	chr3:61544900-61545050	HCM	heart:	n/a	n/a
9	CTCF	chr3:61544880-61545030	GM12874	blood:	n/a	n/a
10	CTCF	chr3:61544940-61545090	AG04450	lung:	n/a	n/a
11	POLR2A	chr3:61544738-61545491	HepG2	liver:	n/a	n/a
12	CTCF	chr3:61545005-61545023	Kidney_OC	kidney:	n/a	n/a
13	CTCF	chr3:61544880-61545030	WERI-Rb-1	eye:	n/a	n/a
14	CTCF	chr3:61544960-61545110	HFF-Myc	foreskin:	n/a	n/a
15	CTCF	chr3:61544920-61545070	NHDF-neo	bronchial:	n/a	n/a
16	POLR2A	chr3:61544864-61554855	MCF10A-Er-Src	breast:	n/a	n/a
17	CTCF	chr3:61544880-61545030	HPF	lung:	n/a	n/a
18	RAD21	chr3:61544817-61545056	HepG2	liver:	n/a	n/a
19	MAFK	chr3:61545011-61545210	HepG2	liver:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:61541363..61545409-chr3:61545583..61548750,5	MCF-7	breast:
2	chr3:61538544..61540472-chr3:61544545..61547220,2	K562	blood:

No data

Variant related genes	Relation type
PTPRG	TF binding region
ENSG00000144724	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11130848	0.85[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.86[ASN][1000 genomes]
rs11709537	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.84[ASN][1000 genomes]
rs28393212	0.89[ASN][1000 genomes]
rs28439601	0.85[ASN][1000 genomes]
rs2886517	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4536820	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56172395	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56259257	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58068671	0.87[EUR][1000 genomes]
rs62243001	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62243002	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62243003	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62243004	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6445225	0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[ASN][1000 genomes]
rs6773372	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6780796	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6785899	0.84[ASN][1000 genomes]
rs6809260	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73093085	0.92[ASN][1000 genomes]
rs73093091	0.92[ASN][1000 genomes]
rs73093101	0.90[ASN][1000 genomes]
rs7626163	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7627324	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7649091	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7649299	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs938959	0.85[CHB][hapmap]
rs9828525	0.85[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs9855083	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9865034	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9865322	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9870074	0.91[EUR][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	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv822105	chr3:61531517-61556259	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv1841066	chr3:61534766-61550452	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	esv3351193	chr3:61544484-61545022	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61542200-61545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:61543800-61545400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:61544600-61545400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:61544800-61545200	Enhancers	H9 Cell Line	embryonic stem cell
5	chr3:61544800-61545200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:61544800-61545200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr3:61544800-61545400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:61544800-61545400	Enhancers	Placenta	Placenta
9	chr3:61545000-61545200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:61545000-61545200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:61545000-61545200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:61545000-61545200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:61545000-61545200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
14	chr3:61545000-61545200	Enhancers	Right Atrium	heart
15	chr3:61545000-61545200	Enhancers	Right Ventricle	heart
16	chr3:61545000-61545200	Enhancers	HepG2	liver
17	chr3:61545000-61545400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:61545000-61545400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr3:61545000-61545400	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:61545000-61545400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr3:61545000-61545400	Enhancers	Left Ventricle	heart
22	chr3:61545000-61545400	Enhancers	HUVEC	blood vessel
23	chr3:61545000-61545400	Enhancers	NHLF	lung
24	chr3:61545000-61545600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr3:61545000-61545600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:61545000-61545600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:61545000-61545600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr3:61545000-61545600	Enhancers	Fetal Kidney	kidney
29	chr3:61545000-61545600	Enhancers	Fetal Muscle Leg	muscle
30	chr3:61545000-61545600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr3:61545000-61545600	Enhancers	NHDF-Ad	bronchial
32	chr3:61545000-61545800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr3:61545000-61545800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:61545000-61545800	Flanking Active TSS	Osteobl	bone
35	chr3:61545000-61546000	Enhancers	Fetal Heart	heart
36	chr3:61545000-61547800	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr3:61545000-61549600	Active TSS	NHEK	skin
38	chr3:61545000-61550800	Active TSS	Psoas Muscle	Psoas

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