Variant report

Variant	rs11130848
Chromosome Location	chr3:61546916-61546917
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr3:61546454-61547375	H1-neurons	neurons:	n/a	n/a
2	RCOR1	chr3:61546162-61547407	HepG2	liver:	n/a	n/a
3	MAX	chr3:61546363-61547693	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr3:61546837-61547531	A549	lung:	n/a	n/a
5	ARID3A	chr3:61546348-61547410	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:61546340-61547427	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:61546836-61547437	SK-N-MC	brain:	n/a	n/a
8	SP1	chr3:61546324-61546923	HepG2	liver:	n/a	chr3:61546593-61546604 chr3:61546595-61546604 chr3:61546624-61546645
9	REST	chr3:61545978-61551180	H1-neurons	neurons:	n/a	chr3:61549601-61549619 chr3:61549134-61549147 chr3:61546464-61546474 chr3:61548149-61548162 chr3:61548255-61548268 chr3:61550446-61550459 chr3:61549161-61549170 chr3:61546827-61546840 chr3:61546361-61546371 chr3:61546824-61546833
10	NFIC	chr3:61545976-61547740	SK-N-SH	brain:	n/a	n/a
11	ZBTB7A	chr3:61546678-61547756	ECC-1	luminal epithelium:	n/a	n/a
12	CTBP2	chr3:61546260-61547603	H1-hESC	embryonic stem cell:	n/a	n/a
13	SIN3A	chr3:61546797-61547446	GM12878	blood:	n/a	chr3:61546824-61546837
14	MAX	chr3:61546898-61547444	GM12878	blood:	n/a	n/a
15	MAX	chr3:61546312-61547754	HepG2	liver:	n/a	n/a
16	YY1	chr3:61546229-61547839	HepG2	liver:	n/a	chr3:61546593-61546604 chr3:61546451-61546460
17	YY1	chr3:61546179-61547616	SK-N-SH	brain:	n/a	chr3:61546593-61546604 chr3:61546451-61546460
18	POLR2A	chr3:61546293-61547638	MCF-7	breast:	n/a	n/a
19	POLR2A	chr3:61546181-61547561	ECC-1	luminal epithelium:	n/a	n/a
20	TCF12	chr3:61546099-61547551	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr3:61546090-61547498	HepG2	liver:	n/a	n/a
22	RFX5	chr3:61546370-61547311	HepG2	liver:	n/a	n/a
23	EP300	chr3:61546009-61548004	SK-N-SH	brain:	n/a	chr3:61546642-61546656 chr3:61546644-61546658 chr3:61546392-61546408 chr3:61546393-61546409 chr3:61546641-61546655 chr3:61546652-61546666
24	POLR2A	chr3:61546113-61547426	GM12878	blood:	n/a	n/a
25	MAZ	chr3:61546206-61547604	GM12878	blood:	n/a	n/a
26	MYC	chr3:61546254-61547409	MCF10A-Er-Src	breast:	n/a	n/a
27	TAF7	chr3:61546864-61547500	H1-hESC	embryonic stem cell:	n/a	n/a
28	CEBPB	chr3:61546164-61547245	H1-hESC	embryonic stem cell:	n/a	chr3:61546567-61546576 chr3:61546565-61546576 chr3:61546567-61546576 chr3:61546567-61546576
29	GATA3	chr3:61545885-61547605	SK-N-SH	brain:	n/a	chr3:61546300-61546310 chr3:61546300-61546309 chr3:61546300-61546309 chr3:61546301-61546309
30	PBX3	chr3:61546112-61547479	SK-N-SH	brain:	n/a	chr3:61546626-61546635
31	KAP1	chr3:61546038-61547507	HEK293	kidney:	n/a	n/a
32	POLR2A	chr3:61546219-61547770	HepG2	liver:	n/a	n/a
33	MAX	chr3:61546152-61547536	SK-N-SH	brain:	n/a	n/a
34	BACH1	chr3:61546913-61546993	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr3:61546840-61547624	H1-hESC	embryonic stem cell:	n/a	chr3:61546977-61546990
36	POLR2A	chr3:61546151-61547406	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr3:61546318-61547818	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr3:61546907-61547413	HepG2	liver:	n/a	n/a
39	TCF7L2	chr3:61546732-61547427	PANC-1	pancreas:	n/a	n/a
40	FOXM1	chr3:61546090-61546952	ECC-1	luminal epithelium:	n/a	n/a
41	HEY1	chr3:61546041-61547582	HepG2	liver:	n/a	n/a
42	E2F6	chr3:61546863-61547477	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr3:61546623-61547442	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:61546881-61547389	GM12891	blood:	n/a	n/a
45	GATA2	chr3:61545981-61547062	SH-SY5Y	brain:	n/a	chr3:61546300-61546310 chr3:61546300-61546309 chr3:61546300-61546309
46	POLR2A	chr3:61545975-61547574	GM12892	blood:	n/a	n/a
47	MAZ	chr3:61546214-61547420	HepG2	liver:	n/a	n/a
48	POLR2A	chr3:61546287-61547584	Gliobla	brain:	n/a	n/a
49	POLR2A	chr3:61546163-61547436	GM12892	blood:	n/a	n/a
50	CHD1	chr3:61546000-61548206	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:234744695..234746368-chr3:61546699..61548508,2	MCF-7	breast:
2	chr3:61538544..61540472-chr3:61544545..61547220,2	K562	blood:

Variant related genes	Relation type
PTPRG	TF binding region
ENSG00000168264	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11709537	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28393212	0.90[ASN][1000 genomes]
rs28439601	0.87[ASN][1000 genomes]
rs6445225	0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6785899	0.85[ASN][1000 genomes]
rs73093085	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73093091	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73093101	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs938959	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9828525	0.82[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs9851992	0.85[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv1837343	chr3:61546425-61550452	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	esv20235	chr3:61546427-61550555	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
8	esv3375328	chr3:61546437-61549285	Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61545000-61547800	Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr3:61545000-61549600	Active TSS	NHEK	skin
3	chr3:61545000-61550800	Active TSS	Psoas Muscle	Psoas
4	chr3:61545200-61549400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:61545400-61549000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:61545400-61549600	Active TSS	Duodenum Mucosa	Duodenum
7	chr3:61545400-61550400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr3:61545400-61550800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:61545400-61550800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:61545400-61550800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:61545600-61547000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:61545600-61547000	Active TSS	Brain Hippocampus Middle	brain
13	chr3:61545600-61547800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr3:61545600-61548200	Active TSS	Fetal Brain Female	brain
15	chr3:61545600-61548400	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr3:61545600-61548400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:61545600-61548400	Active TSS	Fetal Muscle Trunk	muscle
18	chr3:61545600-61548400	Active TSS	Placenta	Placenta
19	chr3:61545600-61548400	Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr3:61545600-61549000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:61545600-61549000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:61545600-61549000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:61545600-61549000	Active TSS	Liver	Liver
24	chr3:61545600-61549200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:61545600-61549200	Active TSS	Fetal Lung	lung
26	chr3:61545600-61549400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr3:61545600-61549400	Active TSS	Brain Angular Gyrus	brain
28	chr3:61545600-61549400	Active TSS	Fetal Brain Male	brain
29	chr3:61545600-61549600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:61545600-61549600	Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr3:61545600-61549800	Active TSS	HSMM	muscle
32	chr3:61545600-61550200	Active TSS	NHLF	lung
33	chr3:61545600-61550600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:61545600-61550600	Active TSS	Colon Smooth Muscle	Colon
35	chr3:61545600-61550600	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr3:61545600-61550600	Active TSS	NHDF-Ad	bronchial
37	chr3:61545600-61550800	Active TSS	H9 Cell Line	embryonic stem cell
38	chr3:61545600-61550800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:61545600-61550800	Active TSS	Fetal Kidney	kidney
40	chr3:61545600-61550800	Active TSS	Left Ventricle	heart
41	chr3:61545600-61550800	Active TSS	HSMMtube	muscle
42	chr3:61545600-61551000	Active TSS	Aorta	Aorta
43	chr3:61545800-61547000	Active TSS	Right Atrium	heart
44	chr3:61545800-61547400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:61545800-61547600	Active TSS	A549	lung
46	chr3:61545800-61547800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:61545800-61548000	Active TSS	Fetal Stomach	stomach
48	chr3:61545800-61548200	Active TSS	Brain Germinal Matrix	brain
49	chr3:61545800-61548400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:61545800-61548400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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