Variant report

Variant	rs6657898
Chromosome Location	chr1:212872931-212872932
allele	A/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	CTCF	chr1:212872214-212873001	GM19238	blood:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
2	YY1	chr1:212872489-212872989	GM12878	blood:	n/a	n/a
3	TEAD4	chr1:212872482-212873026	H1-hESC	embryonic stem cell:	n/a	n/a
4	RUNX3	chr1:212872258-212872987	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:212872290-212874139	GM18505	blood:	n/a	n/a
6	CTCF	chr1:212872144-212872964	H1-hESC	embryonic stem cell:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
7	GABPA	chr1:212872519-212872978	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr1:212872600-212872959	K562	blood:	n/a	n/a
9	MXI1	chr1:212872283-212874137	GM12878	blood:	n/a	chr1:212873444-212873453
10	JUND	chr1:212872408-212873016	H1-hESC	embryonic stem cell:	n/a	n/a
11	YY1	chr1:212872528-212872974	H1-hESC	embryonic stem cell:	n/a	n/a
12	BHLHE40	chr1:212872324-212874972	GM12878	blood:	n/a	chr1:212873287-212873303 chr1:212874387-212874396
13	BHLHE40	chr1:212872366-212873026	K562	blood:	n/a	n/a
14	MAX	chr1:212872288-212873571	K562	blood:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
15	RAD21	chr1:212872256-212872959	H1-hESC	embryonic stem cell:	n/a	chr1:212872768-212872780 chr1:212872514-212872528 chr1:212872520-212872530
16	ZMIZ1	chr1:212872682-212872943	K562	blood:	n/a	n/a
17	CTCF	chr1:212872277-212872954	K562	blood:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
18	POLR2A	chr1:212872554-212873048	GM12892	blood:	n/a	n/a
19	MAX	chr1:212872192-212873716	ECC-1	luminal epithelium:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
20	E2F6	chr1:212872202-212874716	A549	lung:	n/a	chr1:212874470-212874477 chr1:212873219-212873229 chr1:212873421-212873431 chr1:212874470-212874477 chr1:212873224-212873233 chr1:212873180-212873190 chr1:212874470-212874477
21	CTCF	chr1:212872120-212873181	K562	blood:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
22	RAD21	chr1:212872395-212872996	H1-hESC	embryonic stem cell:	n/a	chr1:212872768-212872780 chr1:212872514-212872528 chr1:212872520-212872530
23	MYC	chr1:212871994-212874245	A549	lung:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
24	MAX	chr1:212872207-212875186	NB4	blood:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212874385-212874396 chr1:212872701-212872710 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873986-212873995 chr1:212873443-212873451 chr1:212874394-212874404 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
25	CHD2	chr1:212872544-212873042	Hela-S3	cervix:	n/a	chr1:212872948-212872958
26	CTCF	chr1:212872361-212872939	A549	lung:	n/a	chr1:212872514-212872527 chr1:212872605-212872614 chr1:212872514-212872532 chr1:212872517-212872530 chr1:212872765-212872778 chr1:212872762-212872780
27	TEAD4	chr1:212872552-212873050	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr1:212872526-212873389	Hela-S3	cervix:	n/a	chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212872699-212872714 chr1:212872700-212872710
29	MAX	chr1:212872227-212873605	HepG2	liver:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
30	RAD21	chr1:212872207-212872953	HepG2	liver:	n/a	chr1:212872768-212872780 chr1:212872514-212872528 chr1:212872520-212872530
31	MAX	chr1:212872058-212873687	H1-hESC	embryonic stem cell:	n/a	chr1:212873445-212873454 chr1:212873323-212873333 chr1:212872700-212872711 chr1:212872702-212872709 chr1:212873225-212873235 chr1:212872701-212872710 chr1:212873443-212873451 chr1:212873444-212873455 chr1:212873445-212873454 chr1:212872699-212872714 chr1:212873444-212873455 chr1:212872700-212872710 chr1:212873445-212873454
32	CCNT2	chr1:212872522-212873305	K562	blood:	n/a	chr1:212873224-212873233
33	RFX5	chr1:212872923-212872959	HepG2	liver:	n/a	n/a
34	JUND	chr1:212872355-212873113	A549	lung:	n/a	n/a
35	POLR2A	chr1:212872274-212874715	GM19193	blood:	n/a	n/a
36	RAD21	chr1:212872102-212873006	H1-hESC	embryonic stem cell:	n/a	chr1:212872768-212872780 chr1:212872514-212872528 chr1:212872520-212872530
37	RCOR1	chr1:212872383-212873023	K562	blood:	n/a	n/a
38	MAZ	chr1:212872509-212873062	HepG2	liver:	n/a	chr1:212872700-212872711 chr1:212872702-212872709 chr1:212872701-212872710 chr1:212872699-212872714 chr1:212872700-212872710
39	E2F6	chr1:212872879-212873604	K562	blood:	n/a	chr1:212873219-212873229 chr1:212873421-212873431 chr1:212873224-212873233 chr1:212873180-212873190
40	POLR2A	chr1:212872537-212872964	HCT-116	colon:	n/a	n/a
41	BACH1	chr1:212872523-212874997	H1-hESC	embryonic stem cell:	n/a	n/a
42	YY1	chr1:212872306-212873196	K562	blood:	n/a	n/a
43	YY1	chr1:212872548-212873184	ECC-1	luminal epithelium:	n/a	n/a
44	SIN3AK20	chr1:212872527-212873038	K562	blood:	n/a	n/a
45	TCF7L2	chr1:212872270-212873225	HCT-116	colon:	n/a	n/a
46	POLR2A	chr1:212872235-212874091	GM12892	blood:	n/a	n/a
47	CTCF	chr1:212872720-212872990	NHEK	skin:	n/a	chr1:212872765-212872778 chr1:212872762-212872780
48	CEBPB	chr1:212872775-212873286	A549	lung:	n/a	n/a
49	E2F6	chr1:212872021-212873826	H1-hESC	embryonic stem cell:	n/a	chr1:212873219-212873229 chr1:212873421-212873431 chr1:212873224-212873233 chr1:212873180-212873190
50	FOXM1	chr1:212872449-212873080	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212779956..212785175-chr1:212870276..212874748,7	K562	blood:
2	chr1:212780968..212782915-chr1:212872894..212874871,2	MCF-7	breast:
3	chr1:212872476..212873206-chr1:213140873..213141422,2	K562	blood:
4	chr1:212872473..212873111-chr1:212955524..212956225,2	MCF-7	breast:
5	chr1:212872567..212873252-chr1:212955508..212956261,2	K562	blood:
6	chr1:212779956..212783547-chr1:212870276..212874584,4	K562	blood:
7	chr1:212872500..212873127-chr1:212891520..212892244,2	MCF-7	breast:

Variant related genes	Relation type
BATF3	TF binding region
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs56085986	1.00[AMR][1000 genomes]
rs58402000	1.00[AMR][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	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv1829918	chr1:212828460-212874731	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr1:212871800-212873000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
2	chr1:212871800-212873200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:212872000-212873000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr1:212872000-212873000	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr1:212872000-212873000	Bivalent Enhancer	Stomach Mucosa	stomach
6	chr1:212872000-212873000	Flanking Bivalent TSS/Enh	Thymus	Thymus
7	chr1:212872000-212873000	Flanking Bivalent TSS/Enh	NHEK	skin
8	chr1:212872000-212873800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr1:212872000-212874600	Active TSS	Brain Angular Gyrus	brain
10	chr1:212872000-212874800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:212872200-212873000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr1:212872200-212873000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
13	chr1:212872200-212873000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:212872200-212873000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:212872200-212873000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
19	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
20	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
21	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
22	chr1:212872200-212873000	Bivalent Enhancer	Fetal Lung	lung
23	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
24	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
25	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
26	chr1:212872200-212873000	Flanking Active TSS	Left Ventricle	heart
27	chr1:212872200-212873000	Flanking Active TSS	Lung	lung
28	chr1:212872200-212873000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
29	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
30	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
31	chr1:212872200-212873000	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr1:212872200-212873000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
33	chr1:212872200-212873800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr1:212872200-212873800	Flanking Bivalent TSS/Enh	Dnd41	blood
35	chr1:212872200-212874000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:212872200-212874000	Flanking Active TSS	Right Ventricle	heart
37	chr1:212872200-212874000	Flanking Bivalent TSS/Enh	HMEC	breast
38	chr1:212872200-212874600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr1:212872200-212874600	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr1:212872200-212874600	Bivalent Enhancer	Fetal Brain Male	brain
41	chr1:212872200-212874600	Active TSS	A549	lung
42	chr1:212872200-212874800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
43	chr1:212872200-212874800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr1:212872200-212874800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr1:212872200-212874800	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr1:212872400-212873000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:212872400-212873000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:212872400-212873000	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
49	chr1:212872400-212873000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
50	chr1:212872400-212873000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links