Variant report

Variant	rs3774758
Chromosome Location	chr3:49938227-49938228
allele	C/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	FOXA1	chr3:49938210-49938539	T-47D	breast:	n/a	n/a
2	FOSL2	chr3:49938004-49938544	A549	lung:	n/a	chr3:49938126-49938133 chr3:49938126-49938134 chr3:49938126-49938134
3	POLR2A	chr3:49937782-49938960	Hela-S3	cervix:	n/a	n/a
4	TBP	chr3:49937802-49938630	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:49938024-49938651	MCF-7	breast:	n/a	n/a
6	SP1	chr3:49937702-49938898	HCT-116	colon:	n/a	n/a
7	SMARCB1	chr3:49937712-49938715	Hela-S3	cervix:	n/a	n/a
8	MAX	chr3:49937816-49938630	Hela-S3	cervix:	n/a	chr3:49938126-49938135
9	FOS	chr3:49937950-49938585	MCF10A-Er-Src	breast:	n/a	chr3:49938126-49938133 chr3:49938126-49938134 chr3:49938126-49938134
10	FOS	chr3:49937907-49938891	Hela-S3	cervix:	n/a	chr3:49938126-49938133 chr3:49938126-49938134 chr3:49938126-49938134
11	CTCF	chr3:49938180-49938330	K562	blood:	n/a	n/a
12	ZNF143	chr3:49938058-49938520	Hela-S3	cervix:	n/a	n/a
13	TAF1	chr3:49938155-49938646	Hela-S3	cervix:	n/a	n/a
14	STAT3	chr3:49937924-49938539	MCF10A-Er-Src	breast:	n/a	chr3:49938070-49938078
15	MYC	chr3:49937862-49938529	MCF10A-Er-Src	breast:	n/a	chr3:49938126-49938135
16	FOS	chr3:49937822-49938529	MCF10A-Er-Src	breast:	n/a	chr3:49938126-49938133 chr3:49938126-49938134 chr3:49938126-49938134
17	ELK1	chr3:49938054-49938369	Hela-S3	cervix:	n/a	n/a
18	SP1	chr3:49938004-49938692	A549	lung:	n/a	n/a
19	TCF12	chr3:49937782-49938663	ECC-1	luminal epithelium:	n/a	chr3:49938111-49938118
20	TCF12	chr3:49937808-49938687	A549	lung:	n/a	chr3:49938111-49938118
21	FOXA2	chr3:49938006-49938561	A549	lung:	n/a	n/a
22	FOSL2	chr3:49938104-49938608	SK-N-SH	brain:	n/a	chr3:49938126-49938133 chr3:49938126-49938134 chr3:49938126-49938134
23	POLR2A	chr3:49938114-49938631	MCF10A-Er-Src	breast:	n/a	n/a
24	SMARCC1	chr3:49937415-49938985	Hela-S3	cervix:	n/a	n/a
25	ZKSCAN1	chr3:49937841-49938579	Hela-S3	cervix:	n/a	n/a
26	MAFK	chr3:49938067-49938469	Hela-S3	cervix:	n/a	n/a
27	MAX	chr3:49937809-49938575	MCF-7	breast:	n/a	chr3:49938126-49938135
28	MAX	chr3:49937678-49938582	ECC-1	luminal epithelium:	n/a	chr3:49938126-49938135
29	POLR2A	chr3:49937748-49938808	Hela-S3	cervix:	n/a	n/a
30	GTF2F1	chr3:49937953-49938676	Hela-S3	cervix:	n/a	n/a
31	SP1	chr3:49937837-49938672	A549	lung:	n/a	n/a
32	MAX	chr3:49937679-49938733	A549	lung:	n/a	chr3:49938126-49938135
33	MAZ	chr3:49937961-49938600	Hela-S3	cervix:	n/a	chr3:49938126-49938135
34	NFIC	chr3:49937808-49938666	ECC-1	luminal epithelium:	n/a	n/a
35	SIN3AK20	chr3:49938142-49938543	PANC-1	pancreas:	n/a	n/a
36	MYC	chr3:49937918-49938494	MCF10A-Er-Src	breast:	n/a	chr3:49938126-49938135
37	RAD21	chr3:49938153-49938426	A549	lung:	n/a	n/a
38	MXI1	chr3:49937931-49938597	Hela-S3	cervix:	n/a	chr3:49938135-49938144
39	TEAD4	chr3:49937855-49938435	ECC-1	luminal epithelium:	n/a	n/a
40	NFIC	chr3:49937788-49938755	ECC-1	luminal epithelium:	n/a	n/a
41	FOXA2	chr3:49938113-49938592	A549	lung:	n/a	n/a
42	NFIC	chr3:49938052-49938668	SK-N-SH	brain:	n/a	n/a
43	MAX	chr3:49937784-49938573	MCF-7	breast:	n/a	chr3:49938126-49938135
44	SMC3	chr3:49937827-49938596	Hela-S3	cervix:	n/a	n/a
45	TFAP2C	chr3:49937474-49938632	Hela-S3	cervix:	n/a	n/a
46	JUND	chr3:49937924-49938574	Hela-S3	cervix:	n/a	chr3:49938126-49938133 chr3:49938126-49938134 chr3:49938126-49938134
47	POLR2A	chr3:49937746-49939056	HCT-116	colon:	n/a	n/a
48	STAT3	chr3:49937970-49938496	MCF10A-Er-Src	breast:	n/a	chr3:49938070-49938078
49	STAT3	chr3:49937914-49938501	MCF10A-Er-Src	breast:	n/a	chr3:49938070-49938078
50	BRCA1	chr3:49938107-49938435	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49904537..49906285-chr3:49936889..49938764,2	K562	blood:
2	chr3:49839049..49842350-chr3:49936029..49940414,4	K562	blood:
3	chr3:49823044..49824946-chr3:49937035..49939087,2	MCF-7	breast:
4	chr3:49937512..49940184-chr3:49951912..49954370,2	MCF-7	breast:
5	chr3:49844713..49846618-chr3:49938018..49940554,2	K562	blood:
6	chr3:49934674..49936736-chr3:49937436..49939317,2	K562	blood:
7	chr19:3539030..3539554-chr3:49937999..49938700,2	Hela-S3	cervix:
8	chr3:49838036..49840305-chr3:49938057..49940452,2	MCF-7	breast:
9	chr3:49838968..49841390-chr3:49937411..49939491,2	MCF-7	breast:
10	chr3:49932972..49936126-chr3:49936946..49940007,3	MCF-7	breast:
11	chr3:33482406..33483055-chr3:49938128..49938841,2	Hela-S3	cervix:
12	chr3:49840382..49843169-chr3:49936309..49938239,3	K562	blood:
13	chr3:5019914..5020654-chr3:49938057..49938992,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000228008	TF binding region
MST1R	TF binding region
ENSG00000185614	Chromatin interaction
ENSG00000164078	Chromatin interaction
ENSG00000153560	Chromatin interaction
ENSG00000230698	Chromatin interaction
ENSG00000183397	Chromatin interaction
ENSG00000176095	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1062633	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130224	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130226	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11130228	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130229	0.86[ASN][1000 genomes]
rs11130233	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11130234	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11713193	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11713562	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11925192	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12485600	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496973	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13060128	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1317154	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2230590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252833	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2280406	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2353579	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2353586	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2353587	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2526751	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2624843	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2624844	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2681778	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2681780	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2681781	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2777888	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2883057	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34080578	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35065728	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733135	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3774733	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688689	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688690	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688755	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4688756	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4688757	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688758	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55751738	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62262093	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6446187	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6446189	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6446193	0.83[ASN][1000 genomes]
rs6765484	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6767381	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771546	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6772095	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6780731	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6792892	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795703	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72942333	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7609971	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7613875	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621026	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7621352	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7628058	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7634084	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7635002	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9821433	0.84[ASN][1000 genomes]
rs9821675	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9843653	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848497	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9853222	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9861216	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9862795	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9866695	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	47 gene(s)	inside rSNPs	diseases
4	nsv876767	chr3:49918751-50153356	Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs3774758	RBM6	cis	Nerve Tibial	GTEx
rs3774758	FAM212A	cis	Esophagus Mucosa	GTEx
rs3774758	RBM6	cis	Adipose Subcutaneous	GTEx
rs3774758	RBM6	cis	Whole Blood	GTEx
rs3774758	ACTBP13	cis	Skin Sun Exposed Lower leg	GTEx
rs3774758	RBM6	cis	Artery Aorta	GTEx
rs3774758	RBM6	cis	Esophagus Mucosa	GTEx
rs3774758	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs3774758	RBM6	cis	Skin Sun Exposed Lower leg	GTEx
rs3774758	RBM6	cis	Thyroid	GTEx
rs3774758	RBM6	cis	Heart Left Ventricle	GTEx
rs3774758	RBM6	cis	Artery Tibial	GTEx
rs3774758	RBM6	cis	Stomach	GTEx
rs3774758	RBM6	cis	Esophagus Muscularis	GTEx
rs3774758	RBM6	cis	lung	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49920000-49943000	Weak transcription	Brain Anterior Caudate	brain
2	chr3:49920200-49938400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:49925200-49941200	Weak transcription	Brain Germinal Matrix	brain
4	chr3:49926600-49938400	Weak transcription	Aorta	Aorta
5	chr3:49927600-49940400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:49928600-49943000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:49929000-49938400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:49929600-49941200	Weak transcription	Ovary	ovary
9	chr3:49931400-49938400	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:49931400-49943600	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:49933400-49939600	Weak transcription	Fetal Brain Female	brain
12	chr3:49933800-49941400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:49934200-49938600	Weak transcription	Fetal Lung	lung
14	chr3:49934400-49941400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:49935400-49940000	Weak transcription	Spleen	Spleen
16	chr3:49936000-49939000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:49936200-49938800	Transcr. at gene 5' and 3'	NHEK	skin
18	chr3:49936200-49939000	Enhancers	Lung	lung
19	chr3:49936200-49941000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:49936400-49940800	Enhancers	Pancreas	Pancrea
21	chr3:49936800-49939600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:49937000-49940800	Enhancers	Sigmoid Colon	Sigmoid Colon
23	chr3:49937400-49940200	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr3:49937600-49938800	Enhancers	Placenta Amnion	Placenta Amnion
25	chr3:49937600-49938800	Flanking Active TSS	A549	lung
26	chr3:49937600-49939000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:49937600-49940800	Enhancers	K562	blood
28	chr3:49937600-49941000	Enhancers	Placenta	Placenta
29	chr3:49937600-49943200	Active TSS	Rectal Smooth Muscle	rectum
30	chr3:49937800-49938600	Weak transcription	Gastric	stomach
31	chr3:49937800-49938800	Enhancers	NH-A	brain
32	chr3:49937800-49939000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:49937800-49939000	Enhancers	HSMM	muscle
34	chr3:49937800-49939000	Enhancers	Osteobl	bone
35	chr3:49937800-49939200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:49937800-49939400	Enhancers	Small Intestine	intestine
37	chr3:49937800-49940400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:49938000-49938400	Active TSS	Duodenum Mucosa	Duodenum
39	chr3:49938000-49938600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:49938000-49938600	Enhancers	Stomach Mucosa	stomach
41	chr3:49938000-49938600	Active TSS	Hela-S3	cervix
42	chr3:49938000-49939000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:49938000-49939000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:49938000-49939200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:49938000-49939400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr3:49938000-49939600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:49938000-49940000	Genic enhancers	Fetal Intestine Small	intestine
48	chr3:49938000-49941400	Enhancers	GM12878-XiMat	blood
49	chr3:49938200-49938400	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr3:49938200-49938400	Flanking Bivalent TSS/Enh	HepG2	liver

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