Variant report

Variant	rs1476852
Chromosome Location	chr6:57181847-57181848
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:221)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:221 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:57181780-57181930	NHEK	skin:	n/a	n/a
2	POLR2A	chr6:57181449-57181893	K562	blood:	n/a	n/a
3	RAD21	chr6:57181211-57181975	SK-N-SH_RA	brain:	n/a	n/a
4	E2F6	chr6:57181353-57182026	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr6:57181239-57181971	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:57181405-57182752	HepG2	liver:	n/a	n/a
7	SIN3A	chr6:57181317-57182994	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAX	chr6:57181183-57181853	MCF-7	breast:	n/a	n/a
9	CTCF	chr6:57181750-57181854	MCF-7	breast:	n/a	n/a
10	RAD21	chr6:57181101-57181964	H1-hESC	embryonic stem cell:	n/a	n/a
11	TBP	chr6:57181291-57182845	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr6:57181740-57181890	HepG2	liver:	n/a	n/a
13	JUND	chr6:57181302-57182639	K562	blood:	n/a	n/a
14	POLR2A	chr6:57181490-57182660	HCT-116	colon:	n/a	n/a
15	CTCF	chr6:57181780-57181930	GM12873	blood:	n/a	n/a
16	CTCF	chr6:57181820-57181970	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr6:57181336-57182728	K562	blood:	n/a	n/a
18	POLR2A	chr6:57181406-57182690	GM12892	blood:	n/a	n/a
19	RELA	chr6:57181295-57183003	GM15510	blood:	n/a	n/a
20	MAX	chr6:57181220-57181980	SK-N-SH	brain:	n/a	n/a
21	MAX	chr6:57181163-57182020	HepG2	liver:	n/a	n/a
22	MAX	chr6:57181158-57182915	HCT-116	colon:	n/a	n/a
23	CTCF	chr6:57181177-57182675	SK-N-SH	brain:	n/a	n/a
24	SIN3AK20	chr6:57181379-57181864	PFSK-1	brain:	n/a	n/a
25	E2F6	chr6:57181377-57183006	K562	blood:	n/a	chr6:57182070-57182087 chr6:57182435-57182447
26	CTCF	chr6:57181740-57181890	HBMEC	blood vessel:	n/a	n/a
27	E2F4	chr6:57181313-57182968	MCF10A-Er-Src	breast:	n/a	chr6:57182070-57182087 chr6:57182434-57182445 chr6:57182435-57182447
28	UBTF	chr6:57181405-57181862	K562	blood:	n/a	n/a
29	POLR2A	chr6:57181346-57182977	K562	blood:	n/a	n/a
30	CTCF	chr6:57181713-57181874	GM19238	blood:	n/a	n/a
31	SPI1	chr6:57181208-57181970	HL-60	blood:	n/a	chr6:57181757-57181764
32	ZNF143	chr6:57181273-57182189	K562	blood:	n/a	n/a
33	ATF2	chr6:57181338-57181860	GM12878	blood:	n/a	n/a
34	RAD21	chr6:57181183-57181985	IMR90	lung:	n/a	n/a
35	SMC3	chr6:57181212-57182655	Hela-S3	cervix:	n/a	n/a
36	NRF1	chr6:57181390-57182647	GM12878	blood:	n/a	chr6:57182329-57182343 chr6:57182329-57182340
37	SPI1	chr6:57181377-57181899	GM12891	blood:	n/a	chr6:57181757-57181764
38	MXI1	chr6:57181158-57183337	SK-N-SH	brain:	n/a	n/a
39	MAX	chr6:57181300-57182671	A549	lung:	n/a	n/a
40	TCF7L2	chr6:57181217-57181903	PANC-1	pancreas:	n/a	n/a
41	CTCF	chr6:57181739-57181860	GM12878	blood:	n/a	n/a
42	TEAD4	chr6:57181248-57181938	K562	blood:	n/a	n/a
43	POLR2A	chr6:57181324-57183072	GM12891	blood:	n/a	n/a
44	MXI1	chr6:57181072-57182912	IMR90	lung:	n/a	n/a
45	CTCF	chr6:57181739-57181859	MCF-7	breast:	n/a	n/a
46	CEBPB	chr6:57181360-57181857	K562	blood:	n/a	n/a
47	CTCF	chr6:57181740-57181890	HPAF	blood vessel:	n/a	n/a
48	MAX	chr6:57181297-57181929	K562	blood:	n/a	n/a
49	STAT3	chr6:57181322-57181880	MCF10A-Er-Src	breast:	n/a	n/a
50	FOXM1	chr6:57181212-57181979	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:57181802-57181852	SK-N-SH_RA	brain:	n/a
2	chr6:57181802-57181852	GM06990	blood:	n/a
3	chr6:57181802-57181852	H1-hESC	embryonic stem cell:	embryo
4	chr6:57181802-57181852	RPTEC	kidney:	n/a
5	chr6:57181802-57181852	T-47D	breast:	n/a
6	chr6:57181802-57181852	HepG2	liver:	n/a
7	chr6:57181802-57181852	NT2-D1	testis:	n/a
8	chr6:57181802-57181852	HRPEpiC	eye:	n/a
9	chr6:57181802-57181852	HIPEpiC	eye:	n/a
10	chr6:57181802-57181852	HRCEpiC	kidney:	n/a
11	chr6:57181802-57181852	SAEC	small airway:	n/a
12	chr6:57181802-57181852	SKMC	muscle:	n/a
13	chr6:57181802-57181852	BE2_C	brain:	n/a
14	chr6:57181802-57181852	HAEpiC	amniotic membrane:	n/a
15	chr6:57181802-57181852	ProgFib	skin:	n/a
16	chr6:57181802-57181852	AG04450	lung:	fetal
17	chr6:57181802-57181852	NHDF-neo	bronchial:	n/a
18	chr6:57181802-57181852	HL-60	blood:	n/a
19	chr6:57181802-57181852	BJ	skin:	n/a
20	chr6:57181802-57181852	HCF	heart:	n/a
21	chr6:57181802-57181852	K562	blood:	n/a
22	chr6:57181802-57181852	AG09319	gingival:	n/a
23	chr6:57181802-57181852	SK-N-SH	brain:	n/a
24	chr6:57181802-57181852	PrEC	prostate:	n/a
25	chr6:57181802-57181852	HCM	heart:	n/a
26	chr6:57181802-57181852	ovcar-3	ovarian:	n/a
27	chr6:57181802-57181852	HNPCEpiC	eye:	n/a
28	chr6:57181802-57181852	LNCaP	prostate:	n/a
29	chr6:57181802-57181852	Caco-2	colon:	n/a
30	chr6:57181802-57181852	Hepatocyte	liver:	n/a
31	chr6:57181802-57181852	NHBE	bronchial:	n/a
32	chr6:57181802-57181852	AoSMC	blood vessel:	n/a
33	chr6:57181802-57181852	PANC-1	pancreas:	n/a
34	chr6:57181802-57181852	HPAEpiC	pulmonary alveolar:	n/a
35	chr6:57181802-57181852	Jurkat	blood:	n/a
36	chr6:57181802-57181852	Hela-S3	cervix:	n/a
37	chr6:57181802-57181852	GM12892	blood:	n/a
38	chr6:57181802-57181852	NH-A	brain:	n/a
39	chr6:57181802-57181852	HEK293	kidney:	embryo
40	chr6:57181802-57181852	MCF10A-Er-Src	breast:	n/a
41	chr6:57181802-57181852	HRE	kidney:	n/a
42	chr6:57181802-57181852	HMEC	breast:	n/a
43	chr6:57181802-57181852	A549	lung:	n/a
44	chr6:57181802-57181852	HCPEpiC	choroid plexus:	n/a
45	chr6:57181802-57181852	HCT-116	colon:	n/a
46	chr6:57181802-57181852	AG10803	skin:	n/a
47	chr6:57181802-57181852	GM12891	blood:	n/a
48	chr6:57181802-57181852	HEEpiC	esophagus:	n/a
49	chr6:57181802-57181852	HUVEC	blood vessel:	n/a
50	chr6:57181802-57181852	MCF-7	breast:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:57132346..57133175-chr6:57181261..57181900,2	MCF-7	breast:
2	chr6:56818167..56820292-chr6:57177596..57182762,4	MCF-7	breast:
3	chr11:66741225..66741959-chr6:57181813..57182362,2	Hela-S3	cervix:
4	chr6:56917795..56920630-chr6:57180705..57182325,2	K562	blood:
5	chr6:56818015..56821855-chr6:57180367..57183028,4	K562	blood:
6	chr6:57084710..57087719-chr6:57179458..57182091,4	MCF-7	breast:
7	chr6:57054645..57055602-chr6:57180976..57181857,8	MCF-7	breast:
8	chr6:57132738..57133304-chr6:57181110..57181877,2	MCF-7	breast:
9	chr6:57036906..57039086-chr6:57181130..57183954,3	K562	blood:
10	chr6:57054194..57055111-chr6:57181143..57181875,2	K562	blood:
11	chr6:57085596..57088404-chr6:57180850..57182470,2	MCF-7	breast:

No data

Variant related genes	Relation type
PRIM2	TF binding region
PRIM2	CpG island
ENSG00000112208	Chromatin interaction
ENSG00000226803	Chromatin interaction
ENSG00000151917	Chromatin interaction
ENSG00000112210	Chromatin interaction
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12180921	0.81[AFR][1000 genomes]
rs1741910	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1741911	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1741912	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1741913	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1741915	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1755831	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1755832	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1755834	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17705499	0.89[ASN][1000 genomes]
rs1860652	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1888265	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28367021	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28800513	0.86[AFR][1000 genomes]
rs3757295	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3778513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3778514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3800010	0.84[ASN][1000 genomes]
rs4715652	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58482037	0.85[AFR][1000 genomes]
rs6459186	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6459188	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6911353	0.86[AFR][1000 genomes]
rs6915533	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6916106	0.90[EUR][1000 genomes]
rs6936450	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6938582	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7754911	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9396273	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9396274	0.83[EUR][1000 genomes]
rs9464433	0.83[AFR][1000 genomes]
rs9464434	0.86[AFR][1000 genomes]
rs9464437	0.86[AFR][1000 genomes]
rs9464438	0.85[AFR][1000 genomes]
rs9475840	0.86[AFR][1000 genomes]
rs9475841	0.81[AFR][1000 genomes]
rs9475842	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9475844	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9475845	0.86[AFR][1000 genomes]
rs9475847	0.86[AFR][1000 genomes]
rs9475878	0.84[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	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57181000-57183200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr6:57181200-57182000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:57181200-57182600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:57181200-57182600	Active TSS	Primary T cells from cord blood	blood
5	chr6:57181200-57182600	Active TSS	Brain Angular Gyrus	brain
6	chr6:57181200-57182600	Active TSS	Brain Anterior Caudate	brain
7	chr6:57181200-57182600	Active TSS	Brain Cingulate Gyrus	brain
8	chr6:57181200-57182600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:57181200-57182600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:57181200-57182600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr6:57181200-57182600	Active TSS	Right Atrium	heart
12	chr6:57181200-57182800	Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr6:57181200-57182800	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr6:57181200-57183000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr6:57181200-57183200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr6:57181200-57183200	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr6:57181200-57183200	Active TSS	Fetal Brain Female	brain
18	chr6:57181200-57183200	Active TSS	GM12878-XiMat	blood
19	chr6:57181200-57183400	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr6:57181200-57183400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:57181200-57183600	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:57181200-57183800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:57181400-57182000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr6:57181400-57182200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr6:57181400-57182200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr6:57181400-57182600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:57181400-57182600	Active TSS	Primary B cells from peripheral blood	blood
28	chr6:57181400-57182600	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr6:57181400-57182600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr6:57181400-57182600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:57181400-57182600	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr6:57181400-57182600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr6:57181400-57182600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr6:57181400-57182600	Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr6:57181400-57182600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr6:57181400-57182600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr6:57181400-57182600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr6:57181400-57182600	Active TSS	Liver	Liver
39	chr6:57181400-57182600	Active TSS	Brain Germinal Matrix	brain
40	chr6:57181400-57182600	Active TSS	Brain Substantia Nigra	brain
41	chr6:57181400-57182600	Active TSS	Duodenum Mucosa	Duodenum
42	chr6:57181400-57182600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr6:57181400-57182600	Active TSS	Fetal Muscle Leg	muscle
44	chr6:57181400-57182600	Active TSS	Fetal Thymus	thymus
45	chr6:57181400-57182600	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr6:57181400-57182600	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr6:57181400-57182600	Active TSS	HSMMtube	muscle
48	chr6:57181400-57182600	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr6:57181400-57182600	Active TSS	NH-A	brain
50	chr6:57181400-57182800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links