Variant report

Variant	rs4677629
Chromosome Location	chr3:191047966-191047967
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:114)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:114 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:191046911-191047997	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF1	chr3:191046786-191048115	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr3:191046161-191048563	GM19193	blood:	n/a	n/a
4	TAF1	chr3:191047746-191048567	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:191046702-191048304	GM15510	blood:	n/a	n/a
6	MAX	chr3:191046768-191048822	Hela-S3	cervix:	n/a	n/a
7	MAX	chr3:191046631-191048247	HepG2	liver:	n/a	n/a
8	MAX	chr3:191046819-191048142	H1-hESC	embryonic stem cell:	n/a	n/a
9	NFIC	chr3:191046860-191048212	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr3:191046869-191047975	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:191047767-191048063	SK-N-SH	brain:	n/a	n/a
12	ZBTB7A	chr3:191046684-191048113	ECC-1	luminal epithelium:	n/a	n/a
13	CTCF	chr3:191047840-191047990	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:191046549-191048828	HUVEC	blood vessel:	n/a	n/a
15	RELA	chr3:191046517-191048835	GM18951	blood:	n/a	n/a
16	HA-E2F1	chr3:191046077-191048374	MCF-7	breast:	n/a	chr3:191048046-191048058
17	MXI1	chr3:191047769-191049062	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:191046439-191048127	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:191047829-191047974	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr3:191047859-191048295	ProgFib	skin:	n/a	n/a
21	RFX5	chr3:191046576-191049678	Hela-S3	cervix:	n/a	n/a
22	E2F4	chr3:191047549-191048169	MCF10A-Er-Src	breast:	n/a	chr3:191048046-191048058
23	ELK4	chr3:191047896-191048798	Hela-S3	cervix:	n/a	n/a
24	GTF2F1	chr3:191047516-191048903	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr3:191047937-191050305	PFSK-1	brain:	n/a	n/a
26	SIN3A	chr3:191046619-191048409	H1-hESC	embryonic stem cell:	n/a	n/a
27	RCOR1	chr3:191046379-191049021	Hela-S3	cervix:	n/a	n/a
28	MAX	chr3:191046386-191048027	K562	blood:	n/a	n/a
29	CHD1	chr3:191046720-191049324	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:191046465-191048917	Hela-S3	cervix:	n/a	n/a
31	SMC3	chr3:191047778-191049011	Hela-S3	cervix:	n/a	n/a
32	TBP	chr3:191047805-191049575	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr3:191046821-191048720	HUVEC	blood vessel:	n/a	n/a
34	SIN3AK20	chr3:191047607-191048073	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr3:191047749-191048599	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr3:191046459-191049825	IMR90	lung:	n/a	n/a
37	POLR2A	chr3:191046407-191048524	GM18951	blood:	n/a	n/a
38	TBL1XR1	chr3:191047775-191048328	GM12878	blood:	n/a	n/a
39	SIN3AK20	chr3:191047736-191048023	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr3:191046829-191047999	MCF10A-Er-Src	breast:	n/a	n/a
41	MAFK	chr3:191047806-191048757	Hela-S3	cervix:	n/a	chr3:191048280-191048291 chr3:191048366-191048382
42	POLR2A	chr3:191046834-191048009	ECC-1	luminal epithelium:	n/a	n/a
43	PRDM1	chr3:191047882-191048628	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr3:191046781-191048552	K562	blood:	n/a	n/a
45	POLR2A	chr3:191046545-191048343	GM12892	blood:	n/a	n/a
46	SMARCC1	chr3:191046178-191049116	Hela-S3	cervix:	n/a	n/a
47	BHLHE40	chr3:191047768-191048133	K562	blood:	n/a	n/a
48	POLR2A	chr3:191046410-191048195	H1-neurons	neurons:	n/a	n/a
49	BRCA1	chr3:191047888-191049561	Hela-S3	cervix:	n/a	chr3:191048415-191048422
50	MAX	chr3:191047952-191048250	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:190999845..191001643-chr3:191046703..191048798,2	MCF-7	breast:
2	chr12:52463379..52464275-chr3:191047727..191048635,2	Hela-S3	cervix:

No data

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

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16866496	0.99[ASN][1000 genomes]
rs56376956	0.92[ASN][1000 genomes]
rs6801942	0.99[ASN][1000 genomes]
rs709143	0.86[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4677629	CCDC50	cis	Thyroid	GTEx

Chromatin state (count:122 , 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	chr3:191046400-191048200	Active TSS	Rectal Smooth Muscle	rectum
5	chr3:191046400-191048400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:191046400-191048600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:191046400-191048600	Active TSS	Brain Cingulate Gyrus	brain
8	chr3:191046400-191048600	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr3:191046400-191048800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:191046400-191049800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr3:191046600-191048000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:191046600-191048200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
13	chr3:191046600-191048200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:191046600-191048200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:191046600-191048800	Active TSS	Fetal Muscle Trunk	muscle
16	chr3:191046600-191049000	Active TSS	Colonic Mucosa	Colon
17	chr3:191046600-191049000	Active TSS	Fetal Intestine Large	intestine
18	chr3:191046600-191049000	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:191046600-191049000	Active TSS	Left Ventricle	heart
20	chr3:191046600-191049200	Active TSS	HSMM	muscle
21	chr3:191046600-191049600	Active TSS	HSMMtube	muscle
22	chr3:191046600-191049800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:191046600-191049800	Active TSS	Ovary	ovary
24	chr3:191046600-191049800	Active TSS	Right Ventricle	heart
25	chr3:191046600-191050000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:191046600-191050200	Active TSS	Psoas Muscle	Psoas
27	chr3:191046600-191050600	Active TSS	Aorta	Aorta
28	chr3:191046600-191050600	Active TSS	Right Atrium	heart
29	chr3:191046800-191048000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:191046800-191048000	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr3:191046800-191048200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:191046800-191048200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:191046800-191048200	Active TSS	Brain Substantia Nigra	brain
34	chr3:191046800-191048400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:191046800-191048400	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr3:191046800-191048400	Active TSS	Spleen	Spleen
37	chr3:191046800-191048600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:191046800-191048600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:191046800-191048600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr3:191046800-191048600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:191046800-191048600	Active TSS	Pancreas	Pancrea
42	chr3:191046800-191048600	Active TSS	Osteobl	bone
43	chr3:191046800-191048800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr3:191046800-191048800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:191046800-191048800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:191046800-191048800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:191046800-191048800	Active TSS	Primary T helper cells fromperipheralblood	blood
48	chr3:191046800-191048800	Active TSS	Colon Smooth Muscle	Colon
49	chr3:191046800-191048800	Active TSS	Esophagus	oesophagus
50	chr3:191046800-191048800	Active TSS	Fetal Kidney	kidney

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