Variant report

Variant	rs6763138
Chromosome Location	chr3:159482089-159482090
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	STAT3	chr3:159481728-159482104	MCF10A-Er-Src	breast:	n/a	chr3:159482027-159482034
2	SMARCB1	chr3:159480566-159483718	Hela-S3	cervix:	n/a	chr3:159483592-159483601
3	POLR2A	chr3:159480562-159484035	PFSK-1	brain:	n/a	n/a
4	CEBPB	chr3:159480064-159482341	Hela-S3	cervix:	n/a	n/a
5	TBP	chr3:159481916-159482386	Hela-S3	cervix:	n/a	n/a
6	MAX	chr3:159480702-159483613	MCF-7	breast:	n/a	chr3:159481565-159481574 chr3:159482995-159483005 chr3:159483043-159483053
7	TAF1	chr3:159480702-159482392	A549	lung:	n/a	n/a
8	ZNF263	chr3:159480693-159484031	HEK293-T-REx	kidney:	n/a	chr3:159481608-159481617 chr3:159482218-159482227 chr3:159482461-159482482 chr3:159483138-159483147
9	POLR2A	chr3:159478872-159485842	IMR90	lung:	n/a	n/a
10	POLR2A	chr3:159481859-159482383	A549	lung:	n/a	n/a
11	POLR2A	chr3:159480747-159483236	MCF-7	breast:	n/a	n/a
12	CTBP2	chr3:159481920-159483224	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZNF143	chr3:159482065-159482450	Hela-S3	cervix:	n/a	chr3:159482129-159482139
14	SIN3AK20	chr3:159481805-159482274	A549	lung:	n/a	n/a
15	POLR2A	chr3:159480647-159483221	A549	lung:	n/a	n/a
16	SMC3	chr3:159479813-159484045	Hela-S3	cervix:	n/a	chr3:159481356-159481366 chr3:159481836-159481846 chr3:159482090-159482100 chr3:159482126-159482136 chr3:159480742-159480749 chr3:159481981-159481988
17	CTCF	chr3:159482060-159482210	SK-N-SH_RA	brain:	n/a	n/a
18	RFX5	chr3:159481866-159482285	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr3:159480668-159482574	H1-hESC	embryonic stem cell:	n/a	n/a
20	TAF1	chr3:159481429-159482099	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr3:159480666-159482338	HCT-116	colon:	n/a	n/a
22	CHD2	chr3:159481922-159482409	H1-hESC	embryonic stem cell:	n/a	n/a
23	MAFK	chr3:159481895-159482679	Hela-S3	cervix:	n/a	n/a
24	HA-E2F1	chr3:159480802-159483168	Hela-S3	cervix:	n/a	chr3:159481831-159481843 chr3:159481261-159481270 chr3:159481372-159481382 chr3:159483006-159483018 chr3:159481542-159481551 chr3:159481378-159481387 chr3:159482172-159482184 chr3:159480946-159480956 chr3:159482085-159482097
25	POLR2A	chr3:159480483-159482854	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr3:159480675-159484005	Hela-S3	cervix:	n/a	n/a
27	MAX	chr3:159480629-159482348	ECC-1	luminal epithelium:	n/a	chr3:159481565-159481574
28	REST	chr3:159481793-159482292	A549	lung:	n/a	n/a
29	POLR2A	chr3:159480560-159483811	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr3:159480579-159482427	HCT-116	colon:	n/a	n/a
31	POLR2A	chr3:159480606-159482497	Hela-S3	cervix:	n/a	n/a
32	SP1	chr3:159480548-159482516	A549	lung:	n/a	chr3:159481886-159481899 chr3:159481542-159481551 chr3:159481606-159481620 chr3:159481892-159481901 chr3:159481902-159481909 chr3:159482087-159482101 chr3:159481834-159481843 chr3:159482175-159482189 chr3:159481892-159481901 chr3:159481538-159481552 chr3:159481609-159481621 chr3:159481891-159481901 chr3:159482086-159482098 chr3:159482088-159482097 chr3:159481891-159481900
33	BACH1	chr3:159482008-159482200	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr3:159479069-159484734	HUVEC	blood vessel:	n/a	n/a
35	MAX	chr3:159480585-159482561	A549	lung:	n/a	chr3:159481565-159481574
36	TAF1	chr3:159480619-159482529	H1-hESC	embryonic stem cell:	n/a	n/a
37	MXI1	chr3:159480603-159484814	IMR90	lung:	n/a	n/a
38	POLR2A	chr3:159481776-159482460	U87	brain:	n/a	n/a
39	POLR2A	chr3:159481871-159482385	A549	lung:	n/a	n/a
40	TEAD4	chr3:159481787-159482398	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr3:159481853-159482391	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr3:159481788-159483262	ECC-1	luminal epithelium:	n/a	n/a
43	TFAP2C	chr3:159479888-159484192	Hela-S3	cervix:	n/a	chr3:159482066-159482081 chr3:159482088-159482103 chr3:159481475-159481490
44	TAF1	chr3:159480864-159482296	ECC-1	luminal epithelium:	n/a	n/a
45	TAF1	chr3:159481279-159482391	SK-N-SH	brain:	n/a	n/a
46	NR2F2	chr3:159481895-159482546	MCF-7	breast:	n/a	n/a
47	POLR2A	chr3:159480700-159483336	HUVEC	blood vessel:	n/a	n/a
48	GTF2F1	chr3:159481852-159482450	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr3:159481807-159485173	A549	lung:	n/a	chr3:159484740-159484747
50	POLR2A	chr3:159480601-159483832	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:2235486..2236448-chr3:159481582..159482538,2	Hela-S3	cervix:
2	chr3:159481967..159482706-chr9:95432206..95432716,2	Hela-S3	cervix:
3	chr3:159481657..159482253-chrX:133940934..133941497,2	Hela-S3	cervix:

Variant related genes	Relation type
IQCJ-SCHIP1	TF binding region
ENSG00000104886	Chromatin interaction
ENSG00000127080	Chromatin interaction
ENSG00000156500	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10936179	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107061	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715088	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12490735	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491535	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1497762	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1553081	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2010748	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169305	0.87[ASN][1000 genomes]
rs3851359	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3889309	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3889310	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679863	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679865	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680521	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680524	0.94[ASN][1000 genomes]
rs56107912	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62270387	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62270397	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6771478	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6780187	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639937	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3335783	chr3:159480158-159484256	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3426837	chr3:159480283-159483031	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159480000-159483200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
2	chr3:159480400-159483400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr3:159480400-159483800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr3:159480400-159483800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr3:159480400-159483800	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:159480400-159484200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr3:159480600-159483200	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr3:159480600-159483400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr3:159480600-159483400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
10	chr3:159480600-159483600	Active TSS	Psoas Muscle	Psoas
11	chr3:159480600-159483800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:159480600-159483800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:159480600-159483800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr3:159480600-159484000	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr3:159480600-159485400	Active TSS	Aorta	Aorta
16	chr3:159480800-159482200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:159480800-159483200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:159480800-159483400	Active TSS	Fetal Intestine Large	intestine
19	chr3:159480800-159483600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:159480800-159483600	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr3:159480800-159483800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:159480800-159483800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:159480800-159483800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:159480800-159483800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:159480800-159483800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
26	chr3:159480800-159483800	Active TSS	Ovary	ovary
27	chr3:159480800-159483800	Active TSS	A549	lung
28	chr3:159480800-159484000	Active TSS	Left Ventricle	heart
29	chr3:159480800-159484600	Active TSS	Colon Smooth Muscle	Colon
30	chr3:159480800-159485000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:159480800-159485000	Active TSS	Fetal Kidney	kidney
32	chr3:159480800-159485200	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr3:159481000-159482400	Bivalent/Poised TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:159481000-159482800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
35	chr3:159481000-159483200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:159481000-159483200	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr3:159481000-159483400	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr3:159481000-159483400	Active TSS	Brain Substantia Nigra	brain
39	chr3:159481000-159483800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:159481000-159483800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:159481000-159483800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:159481000-159483800	Active TSS	Muscle Satellite Cultured Cells	--
43	chr3:159481000-159483800	Active TSS	Placenta Amnion	Placenta Amnion
44	chr3:159481000-159483800	Active TSS	Rectal Smooth Muscle	rectum
45	chr3:159481000-159484000	Bivalent/Poised TSS	Fetal Stomach	stomach
46	chr3:159481000-159484000	Active TSS	Lung	lung
47	chr3:159481000-159484000	Active TSS	Osteobl	bone
48	chr3:159481000-159484200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:159481000-159484200	Active TSS	NHDF-Ad	bronchial
50	chr3:159481000-159484400	Active TSS	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links