Variant report

Variant	rs980321
Chromosome Location	chr3:191048554-191048555
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:65)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:65 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:191046161-191048563	GM19193	blood:	n/a	n/a
2	TAF1	chr3:191047746-191048567	Hela-S3	cervix:	n/a	n/a
3	FOS	chr3:191048183-191048586	Hela-S3	cervix:	n/a	n/a
4	MAX	chr3:191046768-191048822	Hela-S3	cervix:	n/a	n/a
5	ELK1	chr3:191048175-191048673	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:191046549-191048828	HUVEC	blood vessel:	n/a	n/a
7	RELA	chr3:191046517-191048835	GM18951	blood:	n/a	n/a
8	MXI1	chr3:191047769-191049062	Hela-S3	cervix:	n/a	n/a
9	RFX5	chr3:191046576-191049678	Hela-S3	cervix:	n/a	n/a
10	ELK4	chr3:191047896-191048798	Hela-S3	cervix:	n/a	n/a
11	CUX1	chr3:191047969-191048970	K562	blood:	n/a	n/a
12	GTF2F1	chr3:191047516-191048903	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr3:191047937-191050305	PFSK-1	brain:	n/a	n/a
14	RCOR1	chr3:191046379-191049021	Hela-S3	cervix:	n/a	n/a
15	CHD1	chr3:191046720-191049324	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:191046465-191048917	Hela-S3	cervix:	n/a	n/a
17	SMC3	chr3:191047778-191049011	Hela-S3	cervix:	n/a	n/a
18	ELK1	chr3:191048552-191048566	GM12878	blood:	n/a	n/a
19	TBP	chr3:191047805-191049575	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:191046821-191048720	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr3:191047749-191048599	HUVEC	blood vessel:	n/a	n/a
22	FOS	chr3:191048225-191048818	MCF10A-Er-Src	breast:	n/a	n/a
23	CCNT2	chr3:191048215-191048802	K562	blood:	n/a	n/a
24	POLR2A	chr3:191046459-191049825	IMR90	lung:	n/a	n/a
25	MAFK	chr3:191047806-191048757	Hela-S3	cervix:	n/a	chr3:191048280-191048291 chr3:191048366-191048382
26	EP300	chr3:191048166-191048781	Hela-S3	cervix:	n/a	n/a
27	PRDM1	chr3:191047882-191048628	Hela-S3	cervix:	n/a	n/a
28	SMARCC1	chr3:191046178-191049116	Hela-S3	cervix:	n/a	n/a
29	BRCA1	chr3:191047888-191049561	Hela-S3	cervix:	n/a	chr3:191048415-191048422
30	USF2	chr3:191048204-191048643	Hela-S3	cervix:	n/a	n/a
31	ZKSCAN1	chr3:191046644-191048698	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr3:191046715-191049414	MCF10A-Er-Src	breast:	n/a	n/a
33	CHD2	chr3:191046509-191048808	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr3:191046706-191048729	Hela-S3	cervix:	n/a	n/a
35	TCF7L2	chr3:191047699-191048925	Hela-S3	cervix:	n/a	chr3:191048762-191048778
36	UBTF	chr3:191046251-191048708	K562	blood:	n/a	n/a
37	POLR2A	chr3:191046553-191048734	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:191046524-191048991	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:191046119-191048998	HepG2	liver:	n/a	n/a
40	POLR2A	chr3:191046800-191048836	Hela-S3	cervix:	n/a	n/a
41	EP300	chr3:191047904-191048628	K562	blood:	n/a	n/a
42	RAD21	chr3:191047831-191049236	Hela-S3	cervix:	n/a	n/a
43	MAZ	chr3:191046005-191048601	K562	blood:	n/a	chr3:191046350-191046360
44	RCOR1	chr3:191046313-191048935	K562	blood:	n/a	n/a
45	RAD21	chr3:191046474-191048770	IMR90	lung:	n/a	n/a
46	POLR2A	chr3:191045994-191048586	K562	blood:	n/a	n/a
47	JUN	chr3:191048174-191048579	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr3:191046501-191048672	HUVEC	blood vessel:	n/a	n/a
49	CEBPB	chr3:191047525-191048593	IMR90	lung:	n/a	chr3:191048401-191048412
50	MAZ	chr3:191046379-191048760	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:190999845..191001643-chr3:191046703..191048798,2	MCF-7	breast:
2	chr12:52463379..52464275-chr3:191047727..191048635,2	Hela-S3	cervix:
3	chr3:191044441..191046950-chr3:191048340..191050123,2	K562	blood:

No data

Variant related genes	Relation type
UTS2B	TF binding region
ENSG00000188958	Chromatin interaction
ENSG00000123395	Chromatin interaction
ENSG00000152492	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13326246	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13434281	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17545865	0.94[EUR][1000 genomes]
rs17754685	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17811727	0.96[EUR][1000 genomes]
rs2164237	0.89[EUR][1000 genomes]
rs28368295	0.94[EUR][1000 genomes]
rs28448537	0.94[EUR][1000 genomes]
rs28502671	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28510847	0.95[EUR][1000 genomes]
rs4677634	0.95[EUR][1000 genomes]
rs4687210	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9290985	0.94[EUR][1000 genomes]
rs980320	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9825936	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9826141	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9827142	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9839989	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9844109	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9855282	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9868286	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9868495	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv878101	chr3:190891939-191059322	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv1851611	chr3:191028147-191073560	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv4169	chr3:191036298-191063465	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv3325773	chr3:191046083-191048631	Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv10370	chr3:191046223-191049560	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv980108	chr3:191047936-191051389	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs980321	CCDC50	cis	Nerve Tibial	GTEx
rs980321	CCDC50	cis	Thyroid	GTEx
rs980321	CCDC50	cis	Esophagus Muscularis	GTEx
rs980321	CCDC50	cis	Artery Tibial	GTEx
rs980321	CCDC50	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191046200-191049200	Active TSS	Brain Angular Gyrus	brain
2	chr3:191046200-191049800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:191046200-191049800	Active TSS	Stomach Smooth Muscle	stomach
4	chr3:191046400-191048600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:191046400-191048600	Active TSS	Brain Cingulate Gyrus	brain
6	chr3:191046400-191048600	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr3:191046400-191048800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:191046400-191049800	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr3:191046600-191048800	Active TSS	Fetal Muscle Trunk	muscle
10	chr3:191046600-191049000	Active TSS	Colonic Mucosa	Colon
11	chr3:191046600-191049000	Active TSS	Fetal Intestine Large	intestine
12	chr3:191046600-191049000	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:191046600-191049000	Active TSS	Left Ventricle	heart
14	chr3:191046600-191049200	Active TSS	HSMM	muscle
15	chr3:191046600-191049600	Active TSS	HSMMtube	muscle
16	chr3:191046600-191049800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:191046600-191049800	Active TSS	Ovary	ovary
18	chr3:191046600-191049800	Active TSS	Right Ventricle	heart
19	chr3:191046600-191050000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:191046600-191050200	Active TSS	Psoas Muscle	Psoas
21	chr3:191046600-191050600	Active TSS	Aorta	Aorta
22	chr3:191046600-191050600	Active TSS	Right Atrium	heart
23	chr3:191046800-191048600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:191046800-191048600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:191046800-191048600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:191046800-191048600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:191046800-191048600	Active TSS	Pancreas	Pancrea
28	chr3:191046800-191048600	Active TSS	Osteobl	bone
29	chr3:191046800-191048800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr3:191046800-191048800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:191046800-191048800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:191046800-191048800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:191046800-191048800	Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr3:191046800-191048800	Active TSS	Colon Smooth Muscle	Colon
35	chr3:191046800-191048800	Active TSS	Esophagus	oesophagus
36	chr3:191046800-191048800	Active TSS	Fetal Kidney	kidney
37	chr3:191046800-191048800	Active TSS	Gastric	stomach
38	chr3:191046800-191048800	Active TSS	Small Intestine	intestine
39	chr3:191046800-191048800	Active TSS	NHDF-Ad	bronchial
40	chr3:191046800-191049000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:191046800-191049000	Active TSS	Lung	lung
42	chr3:191046800-191049000	Active TSS	A549	lung
43	chr3:191046800-191049000	Bivalent/Poised TSS	HepG2	liver
44	chr3:191046800-191049400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr3:191046800-191049400	Active TSS	Fetal Brain Female	brain
46	chr3:191046800-191049600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:191046800-191049800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:191047000-191048600	Active TSS	Fetal Intestine Small	intestine
49	chr3:191047000-191048600	Active TSS	Fetal Lung	lung
50	chr3:191047000-191048600	Active TSS	Skeletal Muscle Male	skeletal muscle

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