Variant report

Variant	rs41306506
Chromosome Location	chr9:116343068-116343069
allele	C/T
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	CTCF	chr9:116342960-116343110	SAEC	small airway:	n/a	chr9:116342962-116342980 chr9:116342964-116342977
2	POLR2A	chr9:116342578-116343273	U87	brain:	n/a	n/a
3	NFIC	chr9:116342613-116343386	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr9:116343040-116343190	GM12867	blood:	n/a	n/a
5	POLR2A	chr9:116342817-116343270	MCF10A-Er-Src	breast:	n/a	n/a
6	SPI1	chr9:116342885-116343378	GM12891	blood:	n/a	n/a
7	RUNX3	chr9:116342821-116343301	GM12878	blood:	n/a	n/a
8	GABPA	chr9:116342786-116343470	MCF-7	breast:	n/a	n/a
9	GATA3	chr9:116342733-116343474	MCF-7	breast:	n/a	n/a
10	FOXA1	chr9:116342890-116343256	T-47D	breast:	n/a	n/a
11	NR2F2	chr9:116342673-116343441	MCF-7	breast:	n/a	n/a
12	POLR2A	chr9:116342891-116343412	HL-60	blood:	n/a	n/a
13	SPI1	chr9:116342870-116343336	GM12878	blood:	n/a	n/a
14	HDAC2	chr9:116342847-116343303	MCF-7	breast:	n/a	n/a
15	SPI1	chr9:116342746-116343419	HL-60	blood:	n/a	n/a
16	GABPA	chr9:116342735-116343558	MCF-7	breast:	n/a	n/a
17	POLR2A	chr9:116342984-116343281	MCF-7	breast:	n/a	n/a
18	PBX3	chr9:116342919-116343228	GM12878	blood:	n/a	chr9:116343121-116343130
19	MYC	chr9:116342869-116343217	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr9:116340489-116344674	Raji	blood:	n/a	n/a
21	EBF1	chr9:116342750-116343465	GM12878	blood:	n/a	n/a
22	POLR2A	chr9:116340661-116343385	U87	brain:	n/a	n/a
23	MAX	chr9:116342807-116344605	MCF-7	breast:	n/a	n/a
24	POLR2A	chr9:116342592-116344580	PBDE	blood:	n/a	n/a
25	GATA3	chr9:116342647-116343365	T-47D	breast:	n/a	n/a
26	RUNX3	chr9:116342717-116343279	GM12878	blood:	n/a	n/a
27	MYC	chr9:116342976-116343235	MCF-7	breast:	n/a	n/a
28	EP300	chr9:116342686-116343414	T-47D	breast:	n/a	chr9:116343065-116343079
29	EGR1	chr9:116342736-116343403	MCF-7	breast:	n/a	chr9:116343108-116343118
30	FOXA1	chr9:116342879-116343121	ECC-1	luminal epithelium:	n/a	n/a
31	GATA3	chr9:116342794-116343255	T-47D	breast:	n/a	n/a
32	STAT3	chr9:116342697-116343215	MCF10A-Er-Src	breast:	n/a	n/a
33	NR2F2	chr9:116342719-116343286	MCF-7	breast:	n/a	n/a
34	ELF1	chr9:116342743-116343503	MCF-7	breast:	n/a	n/a
35	ELF1	chr9:116342811-116343476	MCF-7	breast:	n/a	n/a
36	FOS	chr9:116342618-116343141	MCF10A-Er-Src	breast:	n/a	chr9:116343002-116343016
37	POLR2A	chr9:116342849-116343332	MCF-7	breast:	n/a	n/a
38	NFIC	chr9:116342643-116343318	ECC-1	luminal epithelium:	n/a	n/a
39	FOXA1	chr9:116342766-116343288	T-47D	breast:	n/a	n/a
40	POLR2A	chr9:116342957-116343388	MCF-7	breast:	n/a	n/a
41	STAT3	chr9:116342697-116343265	MCF10A-Er-Src	breast:	n/a	n/a
42	FOS	chr9:116342645-116343173	MCF10A-Er-Src	breast:	n/a	chr9:116343002-116343016
43	CTCF	chr9:116342920-116343070	GM12871	blood:	n/a	chr9:116342962-116342980 chr9:116342964-116342977
44	POLR2A	chr9:116341026-116344718	GM12878	blood:	n/a	n/a
45	CEBPB	chr9:116342814-116343321	MCF-7	breast:	n/a	n/a
46	EBF1	chr9:116342805-116343343	GM12878	blood:	n/a	n/a
47	MAX	chr9:116342685-116343400	MCF-7	breast:	n/a	n/a
48	CTCF	chr9:116342940-116343090	HRE	kidney:	n/a	chr9:116342962-116342980 chr9:116342964-116342977
49	MTA3	chr9:116342714-116345297	GM12878	blood:	n/a	n/a
50	ELF1	chr9:116342776-116343620	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:116222989..116229179-chr9:116341260..116348453,12	MCF-7	breast:
2	chr9:116223752..116229757-chr9:116340131..116348699,14	MCF-7	breast:
3	chr9:116101037..116103011-chr9:116343010..116344663,2	MCF-7	breast:
4	chr9:116241552..116244395-chr9:116341689..116345225,3	MCF-7	breast:
5	chr9:116171144..116172776-chr9:116342569..116344666,2	MCF-7	breast:
6	chr9:116169791..116174768-chr9:116341586..116346658,6	MCF-7	breast:

Variant related genes	Relation type
RGS3	TF binding region
ENSG00000148225	Chromatin interaction
ENSG00000138835	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000157653	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10981815	0.86[ASN][1000 genomes]
rs10981830	0.86[ASN][1000 genomes]
rs17525042	0.97[EUR][1000 genomes]
rs17553698	0.97[EUR][1000 genomes]
rs34106027	0.97[EUR][1000 genomes]
rs34142167	0.97[EUR][1000 genomes]
rs35081798	0.97[EUR][1000 genomes]
rs35120599	0.97[EUR][1000 genomes]
rs35329679	0.97[EUR][1000 genomes]
rs3747813	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3810925	0.97[EUR][1000 genomes]
rs3810926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3827674	0.97[EUR][1000 genomes]
rs41276809	0.97[EUR][1000 genomes]
rs41276823	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41312200	1.00[EUR][1000 genomes]
rs41316948	1.00[EUR][1000 genomes]
rs7040635	1.00[ASN][1000 genomes]
rs7049221	1.00[ASN][1000 genomes]
rs72761999	1.00[ASN][1000 genomes]
rs72763841	1.00[ASN][1000 genomes]
rs7854524	1.00[ASN][1000 genomes]
rs883025	0.86[ASN][1000 genomes]
rs884898	0.86[ASN][1000 genomes]
rs9785299	1.00[ASN][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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv893748	chr9:116308709-116421786	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv430093	chr9:116330446-117325446	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41306506	RGS3	cis	Whole Blood	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116335000-116344000	Weak transcription	Ovary	ovary
2	chr9:116335000-116346800	Enhancers	Fetal Heart	heart
3	chr9:116336800-116343400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:116337000-116346400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:116337200-116349600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:116337600-116345800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:116338200-116346000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:116338200-116353600	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr9:116338800-116343200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:116339000-116344000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:116339000-116344000	Enhancers	Brain Cingulate Gyrus	brain
12	chr9:116339000-116344000	Enhancers	NHDF-Ad	bronchial
13	chr9:116339000-116344800	Enhancers	Spleen	Spleen
14	chr9:116339000-116345400	Enhancers	Fetal Muscle Leg	muscle
15	chr9:116339000-116345600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr9:116339200-116345000	Enhancers	Fetal Muscle Trunk	muscle
17	chr9:116339200-116345600	Enhancers	Placenta	Placenta
18	chr9:116339400-116344000	Enhancers	Adipose Nuclei	Adipose
19	chr9:116339400-116344800	Enhancers	Right Atrium	heart
20	chr9:116339600-116343200	Enhancers	Hela-S3	cervix
21	chr9:116339600-116343600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr9:116339600-116343800	Enhancers	Brain Angular Gyrus	brain
23	chr9:116339600-116343800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr9:116339600-116343800	Enhancers	Stomach Mucosa	stomach
25	chr9:116339600-116343800	Enhancers	HUVEC	blood vessel
26	chr9:116339600-116344000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:116339600-116344000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:116339600-116344000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:116339600-116344000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr9:116339600-116344200	Enhancers	Brain Anterior Caudate	brain
31	chr9:116339600-116344200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr9:116339600-116345000	Enhancers	Right Ventricle	heart
33	chr9:116339600-116345000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr9:116339600-116345600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:116339600-116345800	Enhancers	Left Ventricle	heart
36	chr9:116339800-116343800	Enhancers	Fetal Thymus	thymus
37	chr9:116339800-116343800	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr9:116339800-116344000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:116339800-116344000	Enhancers	Colonic Mucosa	Colon
40	chr9:116339800-116344200	Enhancers	Lung	lung
41	chr9:116339800-116344600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr9:116339800-116344600	Enhancers	Esophagus	oesophagus
43	chr9:116339800-116345000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr9:116339800-116345000	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr9:116339800-116345200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr9:116339800-116345200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr9:116340000-116343400	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr9:116340000-116343400	Enhancers	Pancreas	Pancrea
49	chr9:116340200-116355400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr9:116340400-116344000	Enhancers	HSMMtube	muscle

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