Variant report

Variant	rs3777746
Chromosome Location	chr6:35468873-35468874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELK1	chr6:35468870-35468973	Hela-S3	cervix:	n/a	n/a
2	JUN	chr6:35468616-35469006	K562	blood:	n/a	n/a
3	RCOR1	chr6:35468588-35469009	K562	blood:	n/a	n/a
4	MAX	chr6:35468730-35468932	K562	blood:	n/a	n/a
5	JUND	chr6:35468636-35469010	K562	blood:	n/a	n/a
6	FOS	chr6:35468800-35468919	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr6:35465558-35468992	K562	blood:	n/a	n/a
8	JUND	chr6:35468684-35468884	HepG2	liver:	n/a	n/a
9	MAZ	chr6:35468350-35469132	IMR90	lung:	n/a	n/a
10	POLR2A	chr6:35468515-35469156	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr6:35468737-35468944	Hela-S3	cervix:	n/a	n/a
12	USF2	chr6:35468618-35469005	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr6:35468667-35468978	HCT-116	colon:	n/a	n/a
14	ZNF263	chr6:35468540-35469024	HEK293-T-REx	kidney:	n/a	n/a
15	MAZ	chr6:35468640-35468957	K562	blood:	n/a	n/a
16	CEBPB	chr6:35468674-35468949	Hela-S3	cervix:	n/a	n/a
17	TBL1XR1	chr6:35468677-35468924	K562	blood:	n/a	n/a
18	USF1	chr6:35468614-35468912	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:35468418-35468911	K562	blood:	n/a	n/a
20	SMC3	chr6:35468811-35468923	Hela-S3	cervix:	n/a	n/a
21	JUN	chr6:35468465-35469292	K562	blood:	n/a	n/a
22	POLR2A	chr6:35468790-35468964	MCF10A-Er-Src	breast:	n/a	n/a
23	BHLHE40	chr6:35468622-35469097	K562	blood:	n/a	n/a
24	EP300	chr6:35468736-35468875	K562	blood:	n/a	n/a
25	POLR2A	chr6:35468834-35468925	K562	blood:	n/a	n/a
26	USF1	chr6:35468663-35468875	H1-hESC	embryonic stem cell:	n/a	n/a
27	KAP1	chr6:35468350-35469027	U2OS	brain:	n/a	n/a
28	USF1	chr6:35468627-35468950	SK-N-SH	brain:	n/a	n/a
29	USF1	chr6:35468572-35468940	K562	blood:	n/a	n/a
30	RAD21	chr6:35468725-35468894	Hela-S3	cervix:	n/a	n/a
31	BHLHE40	chr6:35468690-35469036	HepG2	liver:	n/a	n/a
32	ATF1	chr6:35468661-35469004	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:35468847-35468897	SKMC	muscle:	n/a
2	chr6:35468847-35468897	HMEC	breast:	n/a
3	chr6:35468847-35468897	HNPCEpiC	eye:	n/a
4	chr6:35468847-35468897	RPTEC	kidney:	n/a
5	chr6:35468847-35468897	HL-60	blood:	n/a
6	chr6:35468847-35468897	SK-N-SH_RA	brain:	n/a
7	chr6:35468847-35468897	GM12892	blood:	n/a
8	chr6:35468847-35468897	NHBE	bronchial:	n/a
9	chr6:35468847-35468897	MCF10A-Er-Src	breast:	n/a
10	chr6:35468847-35468897	ProgFib	skin:	n/a
11	chr6:35468847-35468897	HCPEpiC	choroid plexus:	n/a
12	chr6:35468847-35468897	Hela-S3	cervix:	n/a
13	chr6:35468847-35468897	GM06990	blood:	n/a
14	chr6:35468847-35468897	PANC-1	pancreas:	n/a
15	chr6:35468847-35468897	PFSK-1	brain:	n/a
16	chr6:35468847-35468897	HPAEpiC	pulmonary alveolar:	n/a
17	chr6:35468847-35468897	AG09309	skin:	n/a
18	chr6:35468847-35468897	PrEC	prostate:	n/a
19	chr6:35468847-35468897	K562	blood:	n/a
20	chr6:35468847-35468897	NB4	blood:	n/a
21	chr6:35468847-35468897	HUVEC	blood vessel:	n/a
22	chr6:35468847-35468897	Caco-2	colon:	n/a
23	chr6:35468847-35468897	U87	brain:	n/a
24	chr6:35468847-35468897	Jurkat	blood:	n/a
25	chr6:35468847-35468897	HRPEpiC	eye:	n/a
26	chr6:35468847-35468897	MCF-7	breast:	n/a
27	chr6:35468847-35468897	HEK293	kidney:	embryo
28	chr6:35468847-35468897	AG09319	gingival:	n/a
29	chr6:35468847-35468897	NH-A	brain:	n/a
30	chr6:35468847-35468897	AG04449	skin:	fetal
31	chr6:35468847-35468897	ovcar-3	ovarian:	n/a
32	chr6:35468847-35468897	CMK	blood:	n/a
33	chr6:35468847-35468897	HIPEpiC	eye:	n/a
34	chr6:35468847-35468897	IMR90	lung:	fetal
35	chr6:35468847-35468897	BJ	skin:	n/a
36	chr6:35468847-35468897	AoSMC	blood vessel:	n/a
37	chr6:35468847-35468897	H1-hESC	embryonic stem cell:	embryo
38	chr6:35468847-35468897	HAEpiC	amniotic membrane:	n/a
39	chr6:35468847-35468897	BE2_C	brain:	n/a
40	chr6:35468847-35468897	A549	lung:	n/a
41	chr6:35468847-35468897	GM12878	blood:	n/a
42	chr6:35468847-35468897	AG10803	skin:	n/a
43	chr6:35468847-35468897	HRCEpiC	kidney:	n/a
44	chr6:35468847-35468897	SAEC	small airway:	n/a
45	chr6:35468847-35468897	T-47D	breast:	n/a
46	chr6:35468847-35468897	HRE	kidney:	n/a
47	chr6:35468847-35468897	Hepatocyte	liver:	n/a
48	chr6:35468847-35468897	HCM	heart:	n/a
49	chr6:35468847-35468897	SK-N-MC	brain:	n/a
50	chr6:35468847-35468897	LNCaP	prostate:	n/a

No data

Variant related genes	Relation type
TEAD3	TF binding region
TEAD3	CpG island

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1883636	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067997	1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs3798344	0.82[EUR][1000 genomes]
rs45493300	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4713874	0.89[JPT][hapmap]
rs6928735	0.82[EUR][1000 genomes]
rs6929353	0.83[EUR][1000 genomes]
rs7738975	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7768844	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9689798	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
2	nsv984463	chr6:35432948-35477634	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	67 gene(s)	inside rSNPs	diseases
3	nsv462909	chr6:35457396-35502202	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
4	nsv602912	chr6:35457396-35502202	Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
5	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv1820663	chr6:35464197-35471362	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3777746	GRM4	cis	parietal	SCAN
rs3777746	ANKS1A	cis	cerebellum	SCAN
rs3777746	CPNE5	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35465600-35469200	Enhancers	Fetal Heart	heart
2	chr6:35466400-35469200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:35466400-35469200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:35466400-35476800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:35466400-35479200	Weak transcription	Right Ventricle	heart
6	chr6:35466600-35469000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:35466800-35477000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:35466800-35479400	Weak transcription	Right Atrium	heart
9	chr6:35467000-35473400	Weak transcription	Esophagus	oesophagus
10	chr6:35467200-35469400	Enhancers	Placenta	Placenta
11	chr6:35467400-35478600	Weak transcription	Fetal Lung	lung
12	chr6:35467600-35469200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:35467600-35469200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:35467600-35469200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:35467600-35471600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:35467800-35469200	Enhancers	Left Ventricle	heart
17	chr6:35467800-35469200	Enhancers	Psoas Muscle	Psoas
18	chr6:35468000-35469000	Enhancers	HSMM	muscle
19	chr6:35468000-35469200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:35468000-35469200	Enhancers	Fetal Muscle Trunk	muscle
21	chr6:35468000-35469200	Enhancers	HSMMtube	muscle
22	chr6:35468000-35469200	Enhancers	NHDF-Ad	bronchial
23	chr6:35468200-35469000	Enhancers	Osteobl	bone
24	chr6:35468200-35469200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:35468200-35469200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:35468200-35469200	Enhancers	Hela-S3	cervix
27	chr6:35468400-35469000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
28	chr6:35468400-35469000	Enhancers	H9 Cell Line	embryonic stem cell
29	chr6:35468400-35469000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr6:35468400-35469000	Enhancers	K562	blood
31	chr6:35468400-35469200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr6:35468400-35469200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:35468400-35469800	Bivalent Enhancer	HepG2	liver
34	chr6:35468600-35469000	Enhancers	NH-A	brain
35	chr6:35468600-35469200	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr6:35468600-35469200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:35468600-35469200	Strong transcription	Fetal Stomach	stomach
38	chr6:35468600-35471200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr6:35468600-35471200	Enhancers	Fetal Muscle Leg	muscle
40	chr6:35468800-35469000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr6:35468800-35469000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr6:35468800-35473000	Weak transcription	Placenta Amnion	Placenta Amnion

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