Variant report

Variant	rs28668839
Chromosome Location	chr3:118959315-118959316
allele	A/C
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	POLR2A	chr3:118958863-118960066	GM12878	blood:	n/a	n/a
2	ARID3A	chr3:118958984-118959315	HepG2	liver:	n/a	n/a
3	ZBTB7A	chr3:118959098-118959799	ECC-1	luminal epithelium:	n/a	n/a
4	ZEB1	chr3:118959268-118959996	GM12878	blood:	n/a	n/a
5	NR2F2	chr3:118959062-118959401	K562	blood:	n/a	chr3:118959217-118959232
6	YY1	chr3:118959270-118959827	GM12878	blood:	n/a	chr3:118959671-118959685 chr3:118959766-118959777 chr3:118959674-118959688 chr3:118959514-118959528
7	POLR2A	chr3:118959265-118960069	HUVEC	blood vessel:	n/a	n/a
8	FOXM1	chr3:118958869-118959800	GM12878	blood:	n/a	n/a
9	JUND	chr3:118959171-118960049	A549	lung:	n/a	chr3:118959584-118959593
10	CEBPB	chr3:118959219-118959971	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:118959178-118959980	ECC-1	luminal epithelium:	n/a	n/a
12	USF2	chr3:118959139-118959382	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:118959016-118960030	K562	blood:	n/a	n/a
14	NR2F2	chr3:118958898-118960124	MCF-7	breast:	n/a	chr3:118959217-118959232
15	POLR2A	chr3:118959311-118960142	U87	brain:	n/a	n/a
16	ETS1	chr3:118959086-118959911	A549	lung:	n/a	chr3:118959656-118959669
17	SIN3AK20	chr3:118958869-118960237	MCF-7	breast:	n/a	n/a
18	MTA3	chr3:118958771-118960073	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:118958207-118960535	MCF10A-Er-Src	breast:	n/a	n/a
20	REST	chr3:118958774-118960761	A549	lung:	n/a	n/a
21	MYC	chr3:118958908-118960675	MCF10A-Er-Src	breast:	n/a	n/a
22	USF2	chr3:118959128-118959398	GM12878	blood:	n/a	n/a
23	TBP	chr3:118959180-118960023	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:118959095-118959947	GM12878	blood:	n/a	n/a
25	ZNF143	chr3:118959284-118960109	H1-hESC	embryonic stem cell:	n/a	chr3:118959674-118959684 chr3:118959658-118959676 chr3:118959886-118959896 chr3:118959668-118959678
26	POLR2A	chr3:118959129-118960058	HCT-116	colon:	n/a	n/a
27	MAX	chr3:118959117-118960164	A549	lung:	n/a	n/a
28	POLR2A	chr3:118958869-118960026	A549	lung:	n/a	n/a
29	MYBL2	chr3:118958795-118959377	HepG2	liver:	n/a	n/a
30	NR2F2	chr3:118958991-118959406	K562	blood:	n/a	chr3:118959217-118959232
31	POLR2A	chr3:118959217-118959972	PANC-1	pancreas:	n/a	n/a
32	NR2C2	chr3:118959010-118959703	HepG2	liver:	n/a	chr3:118959217-118959232
33	MAX	chr3:118958795-118960787	A549	lung:	n/a	n/a
34	TCF7L2	chr3:118958925-118960013	Hela-S3	cervix:	n/a	n/a
35	HNF4G	chr3:118958843-118959360	HepG2	liver:	n/a	n/a
36	MAX	chr3:118959041-118960696	NB4	blood:	n/a	n/a
37	MAX	chr3:118959238-118960139	ECC-1	luminal epithelium:	n/a	n/a
38	TBP	chr3:118959219-118959966	K562	blood:	n/a	n/a
39	RELA	chr3:118958993-118960039	GM18951	blood:	n/a	n/a
40	POLR2A	chr3:118959194-118960160	PANC-1	pancreas:	n/a	n/a
41	HEY1	chr3:118958860-118960099	HepG2	liver:	n/a	chr3:118959669-118959684 chr3:118959765-118959780 chr3:118959611-118959626
42	POLR2A	chr3:118959208-118960077	HUVEC	blood vessel:	n/a	n/a
43	MAX	chr3:118958980-118960056	K562	blood:	n/a	n/a
44	E2F6	chr3:118959296-118960130	H1-hESC	embryonic stem cell:	n/a	chr3:118959770-118959780 chr3:118959869-118959876 chr3:118959866-118959877 chr3:118959867-118959877 chr3:118959868-118959876 chr3:118959868-118959876
45	POLR2A	chr3:118959305-118960142	U87	brain:	n/a	n/a
46	USF1	chr3:118959089-118959517	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:118959217-118960080	GM15510	blood:	n/a	n/a
48	USF1	chr3:118959110-118959354	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:118958319-118959995	IMR90	lung:	n/a	n/a
50	REST	chr3:118959300-118959932	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:118957609..118959509-chr3:119217273..119218823,2	MCF-7	breast:
2	chr3:118944759..118947412-chr3:118958236..118960502,3	MCF-7	breast:
3	chr3:118952753..118957545-chr3:118958102..118959880,7	K562	blood:
4	chr3:118948357..118951865-chr3:118958522..118961643,4	MCF-7	breast:
5	chr3:118863527..118866220-chr3:118958408..118962544,4	MCF-7	breast:
6	chr1:22109314..22109945-chr3:118959315..118959846,2	NB4	blood:
7	chr3:118903933..118906787-chr3:118956775..118959458,2	MCF-7	breast:
8	chr3:118948409..118952425-chr3:118955700..118962526,10	K562	blood:
9	chr3:118943120..118945710-chr3:118958108..118960423,2	K562	blood:
10	chr3:118954516..118958209-chr3:118958247..118961418,8	MCF-7	breast:

Variant related genes	Relation type
B4GALT4	TF binding region
ENSG00000240254	Chromatin interaction
ENSG00000144847	Chromatin interaction
ENSG00000090686	Chromatin interaction
ENSG00000163424	Chromatin interaction
ENSG00000113845	Chromatin interaction
ENSG00000121578	Chromatin interaction
ENSG00000114638	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10511384	0.93[ASN][1000 genomes]
rs12690556	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12695382	0.93[ASN][1000 genomes]
rs12695383	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13070981	0.97[ASN][1000 genomes]
rs13091429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13094747	0.93[ASN][1000 genomes]
rs13098659	0.88[ASN][1000 genomes]
rs2001286	0.93[ASN][1000 genomes]
rs28587867	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28885082	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35816234	0.93[ASN][1000 genomes]
rs3752376	0.93[ASN][1000 genomes]
rs3752377	0.93[ASN][1000 genomes]
rs3796358	0.85[ASN][1000 genomes]
rs4687843	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57446248	0.89[ASN][1000 genomes]
rs59140322	0.83[ASN][1000 genomes]
rs59448071	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6808238	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs68103027	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71325367	0.93[ASN][1000 genomes]
rs7650288	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9289125	0.93[ASN][1000 genomes]
rs9812715	0.93[ASN][1000 genomes]
rs9818595	0.92[ASN][1000 genomes]
rs9824387	0.93[ASN][1000 genomes]
rs9832248	0.93[ASN][1000 genomes]
rs9834466	0.90[ASN][1000 genomes]
rs9836230	0.93[ASN][1000 genomes]
rs9837110	0.93[ASN][1000 genomes]
rs9842789	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9844382	0.93[ASN][1000 genomes]
rs9849672	0.91[ASN][1000 genomes]
rs9850349	0.93[ASN][1000 genomes]
rs9857127	0.93[ASN][1000 genomes]
rs9858124	0.90[ASN][1000 genomes]
rs9862321	0.93[ASN][1000 genomes]
rs9867379	0.86[ASN][1000 genomes]
rs9869645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9874573	0.93[ASN][1000 genomes]
rs9879593	0.90[ASN][1000 genomes]
rs9881379	0.93[ASN][1000 genomes]
rs9881947	0.93[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv18354	chr3:118855337-119000251	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv3405597	chr3:118958287-118960835	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118956800-118960000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:118956800-118960000	Active TSS	A549	lung
3	chr3:118957200-118959400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:118957200-118960200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:118957400-118959400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:118957400-118960200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:118957400-118960200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr3:118957400-118960200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:118957400-118960200	Active TSS	NHDF-Ad	bronchial
10	chr3:118957600-118960000	Active TSS	Right Ventricle	heart
11	chr3:118957600-118960200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr3:118957600-118960200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr3:118957600-118960200	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:118957600-118960200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:118957600-118960200	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr3:118957600-118960200	Active TSS	Right Atrium	heart
17	chr3:118957600-118960400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr3:118957800-118959800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:118957800-118959800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:118957800-118960000	Active TSS	H9 Cell Line	embryonic stem cell
21	chr3:118957800-118960000	Active TSS	HSMM	muscle
22	chr3:118957800-118960200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr3:118958000-118959400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr3:118958000-118959400	Flanking Active TSS	Liver	Liver
25	chr3:118958000-118959800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:118958000-118959800	Active TSS	Fetal Intestine Large	intestine
27	chr3:118958000-118959800	Active TSS	HMEC	breast
28	chr3:118958000-118960000	Active TSS	Fetal Stomach	stomach
29	chr3:118958000-118960000	Active TSS	Placenta Amnion	Placenta Amnion
30	chr3:118958000-118960000	Active TSS	GM12878-XiMat	blood
31	chr3:118958000-118960200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr3:118958000-118960200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:118958200-118959400	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr3:118958200-118959800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:118958200-118959800	Active TSS	K562	blood
36	chr3:118958200-118960000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:118958200-118960000	Active TSS	Fetal Intestine Small	intestine
38	chr3:118958200-118960000	Active TSS	Fetal Kidney	kidney
39	chr3:118958200-118960000	Active TSS	Ovary	ovary
40	chr3:118958200-118960200	Active TSS	NHLF	lung
41	chr3:118958400-118959400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr3:118958400-118959400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr3:118958400-118959400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:118958400-118959400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:118958400-118959400	Flanking Active TSS	Dnd41	blood
46	chr3:118958400-118959400	Flanking Active TSS	HUVEC	blood vessel
47	chr3:118958400-118959400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr3:118958400-118959800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:118958400-118959800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:118958400-118959800	Active TSS	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links