Variant report

Variant	rs1108053
Chromosome Location	chr6:30069835-30069836
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:265)
CpG islands
(count:122)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:265 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:30069720-30069870	NHLF	lung:	n/a	n/a
2	MYC	chr6:30069753-30070106	K562	blood:	n/a	n/a
3	POLR2A	chr6:30069591-30070198	U87	brain:	n/a	n/a
4	CTCF	chr6:30069753-30069977	MCF-7	breast:	n/a	n/a
5	BHLHE40	chr6:30069741-30070243	HepG2	liver:	n/a	n/a
6	NFIC	chr6:30069606-30070314	HepG2	liver:	n/a	n/a
7	CTCF	chr6:30069780-30069930	BE2_C	brain:	n/a	n/a
8	MAX	chr6:30069802-30070017	K562	blood:	n/a	n/a
9	POLR2A	chr6:30069597-30070082	Gliobla	brain:	n/a	n/a
10	POLR2A	chr6:30069481-30070354	U87	brain:	n/a	n/a
11	POLR2A	chr6:30069578-30070070	SK-N-MC	brain:	n/a	n/a
12	CTCF	chr6:30069738-30069954	GM19238	blood:	n/a	n/a
13	CTCF	chr6:30069780-30069930	AG10803	skin:	n/a	n/a
14	CTCF	chr6:30069720-30069870	SAEC	small airway:	n/a	n/a
15	ELF1	chr6:30069608-30070396	MCF-7	breast:	n/a	chr6:30070338-30070350 chr6:30070004-30070016
16	ELF1	chr6:30069697-30070148	K562	blood:	n/a	chr6:30070004-30070016
17	MAX	chr6:30069467-30070279	A549	lung:	n/a	n/a
18	CTCF	chr6:30069772-30069943	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:30069661-30069923	H1-hESC	embryonic stem cell:	n/a	n/a
20	CEBPD	chr6:30069675-30069992	HepG2	liver:	n/a	n/a
21	POLR2A	chr6:30069631-30070216	HEK293	kidney:	n/a	n/a
22	CTCF	chr6:30069733-30069933	GM19240	blood:	n/a	n/a
23	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
24	CTCF	chr6:30069760-30069910	HCFaa	heart:	n/a	n/a
25	CTCF	chr6:30069820-30069970	HRPEpiC	eye:	n/a	n/a
26	CTCF	chr6:30069700-30069850	HEEpiC	esophagus:	n/a	n/a
27	POLR2A	chr6:30069820-30069845	IMR90	lung:	n/a	n/a
28	CTCF	chr6:30069780-30069930	GM12870	blood:	n/a	n/a
29	CTCF	chr6:30069780-30069930	WERI-Rb-1	eye:	n/a	n/a
30	CTCF	chr6:30069780-30069930	HPAF	blood vessel:	n/a	n/a
31	CTCF	chr6:30069771-30069932	NHEK	skin:	n/a	n/a
32	CTCF	chr6:30069820-30069970	GM12867	blood:	n/a	n/a
33	CTCF	chr6:30069780-30069930	SK-N-SH_RA	brain:	n/a	n/a
34	MXI1	chr6:30069677-30070146	HepG2	liver:	n/a	n/a
35	SIN3A	chr6:30069652-30070124	H1-hESC	embryonic stem cell:	n/a	n/a
36	PML	chr6:30069579-30070183	MCF-7	breast:	n/a	n/a
37	MXI1	chr6:30069752-30069860	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:30069647-30070182	K562	blood:	n/a	n/a
39	MAZ	chr6:30069697-30070100	K562	blood:	n/a	n/a
40	CTCF	chr6:30069720-30069870	HCM	heart:	n/a	n/a
41	POLR2A	chr6:30069631-30070481	MCF10A-Er-Src	breast:	n/a	n/a
42	MAX	chr6:30069191-30069933	H1-hESC	embryonic stem cell:	n/a	chr6:30069316-30069323 chr6:30069315-30069324
43	ZNF263	chr6:30069497-30070070	HEK293-T-REx	kidney:	n/a	chr6:30069717-30069738
44	CTCF	chr6:30069769-30069958	A549	lung:	n/a	n/a
45	CTCF	chr6:30069710-30069943	Fibrobl	skin:	n/a	n/a
46	CTCF	chr6:30069772-30069953	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr6:30069760-30069910	HCPEpiC	choroid plexus:	n/a	n/a
48	POLR2A	chr6:30069676-30070191	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr6:30069820-30069970	Caco-2	colon:	n/a	n/a
50	CEBPD	chr6:30069671-30070175	HepG2	liver:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30069801-30069851	NHBE	bronchial:	n/a
2	chr6:30069797-30069847	Hepatocyte	liver:	n/a
3	chr6:30069801-30069851	HCPEpiC	choroid plexus:	n/a
4	chr6:30069801-30069851	GM19239	blood:	n/a
5	chr6:30069801-30069851	ECC-1	luminal epithelium:	n/a
6	chr6:30069797-30069847	CMK	blood:	n/a
7	chr6:30069801-30069851	Caco-2	colon:	n/a
8	chr6:30069801-30069851	HMEC	breast:	n/a
9	chr6:30069801-30069851	A549	lung:	n/a
10	chr6:30069797-30069847	MCF-7	breast:	n/a
11	chr6:30069797-30069847	HL-60	blood:	n/a
12	chr6:30069797-30069847	AG04450	lung:	fetal
13	chr6:30069801-30069851	HNPCEpiC	eye:	n/a
14	chr6:30069801-30069851	CMK	blood:	n/a
15	chr6:30069801-30069851	GM06990	blood:	n/a
16	chr6:30069797-30069847	HIPEpiC	eye:	n/a
17	chr6:30069797-30069847	A549	lung:	n/a
18	chr6:30069801-30069851	AG09309	skin:	n/a
19	chr6:30069801-30069851	HCF	heart:	n/a
20	chr6:30069801-30069851	HPAEpiC	pulmonary alveolar:	n/a
21	chr6:30069797-30069847	NHBE	bronchial:	n/a
22	chr6:30069797-30069847	HCM	heart:	n/a
23	chr6:30069801-30069851	MCF10A-Er-Src	breast:	n/a
24	chr6:30069801-30069851	NHDF-neo	bronchial:	n/a
25	chr6:30069801-30069851	U87	brain:	n/a
26	chr6:30069801-30069851	H1-hESC	embryonic stem cell:	embryo
27	chr6:30069797-30069847	GM06990	blood:	n/a
28	chr6:30069801-30069851	AG04449	skin:	fetal
29	chr6:30069797-30069847	AG09309	skin:	n/a
30	chr6:30069797-30069847	K562	blood:	n/a
31	chr6:30069801-30069851	PFSK-1	brain:	n/a
32	chr6:30069797-30069847	SKMC	muscle:	n/a
33	chr6:30069801-30069851	GM12891	blood:	n/a
34	chr6:30069797-30069847	H1-hESC	embryonic stem cell:	embryo
35	chr6:30069797-30069847	PFSK-1	brain:	n/a
36	chr6:30069801-30069851	GM12878	blood:	n/a
37	chr6:30069801-30069851	HEK293	kidney:	embryo
38	chr6:30069801-30069851	SK-N-SH	brain:	n/a
39	chr6:30069797-30069847	NB4	blood:	n/a
40	chr6:30069797-30069847	T-47D	breast:	n/a
41	chr6:30069797-30069847	Hela-S3	cervix:	n/a
42	chr6:30069801-30069851	HUVEC	blood vessel:	n/a
43	chr6:30069797-30069847	HCT-116	colon:	n/a
44	chr6:30069801-30069851	SK-N-SH_RA	brain:	n/a
45	chr6:30069801-30069851	HRCEpiC	kidney:	n/a
46	chr6:30069797-30069847	GM12878	blood:	n/a
47	chr6:30069801-30069851	HL-60	blood:	n/a
48	chr6:30069801-30069851	HAEpiC	amniotic membrane:	n/a
49	chr6:30069797-30069847	RPTEC	kidney:	n/a
50	chr6:30069797-30069847	NT2-D1	testis:	n/a

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30031338..30034907-chr6:30068673..30070684,4	MCF-7	breast:
2	chr20:43514111..43515072-chr6:30069397..30070319,2	Hela-S3	cervix:
3	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
4	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
5	chr10:72575478..72576318-chr6:30069366..30070276,2	Hela-S3	cervix:
6	chr6:30037077..30039641-chr6:30068261..30070312,3	MCF-7	breast:
7	chr6:30027872..30030809-chr6:30069511..30072907,4	K562	blood:
8	chr17:70636264..70637244-chr6:30069427..30070287,2	Hela-S3	cervix:
9	chr6:30069516..30071040-chr6:30137847..30139463,2	MCF-7	breast:
10	chr11:65195679..65196336-chr6:30069510..30070292,2	Hela-S3	cervix:
11	chr6:30068376..30069897-chr6:30103951..30105962,2	MCF-7	breast:
12	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
13	chr17:73720378..73720925-chr6:30069323..30069983,2	HCT-116	colon:
14	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
15	chr6:30027986..30030809-chr6:30067690..30071011,4	K562	blood:
16	chr6:30059663..30061808-chr6:30067229..30070058,2	K562	blood:
17	chr18:12947541..12948216-chr6:30069780..30070632,2	Hela-S3	cervix:
18	chr6:30028086..30030535-chr6:30068315..30071049,3	MCF-7	breast:
19	chr6:30067195..30070112-chr6:30098151..30100617,2	MCF-7	breast:
20	chr6:30069286..30070342-chr6:30364378..30364933,3	K562	blood:
21	chr3:9438250..9438950-chr6:30069636..30070479,2	Hela-S3	cervix:
22	chr6:30039276..30042217-chr6:30067253..30069841,2	K562	blood:
23	chr6:30024946..30027912-chr6:30068442..30070614,2	MCF-7	breast:
24	chr6:30068547..30070487-chr6:30073986..30076858,2	K562	blood:
25	chr6:30063791..30066840-chr6:30067476..30070156,3	MCF-7	breast:
26	chr6:30034219..30034740-chr6:30069488..30070083,2	Hela-S3	cervix:
27	chr6:30067592..30070049-chr6:30312859..30314391,2	K562	blood:
28	chr6:30054838..30057804-chr6:30069131..30071158,2	MCF-7	breast:
29	chr6:30046314..30047956-chr6:30068316..30070912,2	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM31-AS1	TF binding region
TRIM31-AS1	CpG island
ENSG00000206573	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000204616	Chromatin interaction
ENSG00000204614	Chromatin interaction
ENSG00000204619	Chromatin interaction
ENSG00000166913	Chromatin interaction
ENSG00000166224	Chromatin interaction
ENSG00000204610	Chromatin interaction
ENSG00000227036	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000132470	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000252901	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000085415	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10947051	0.81[ASN][1000 genomes]
rs10947052	0.81[ASN][1000 genomes]
rs1108052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1110446	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1110448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1156533	0.91[ASN][1000 genomes]
rs11751554	0.86[ASN][1000 genomes]
rs11753939	0.80[ASN][1000 genomes]
rs11755853	0.81[ASN][1000 genomes]
rs11758516	0.81[ASN][1000 genomes]
rs11965379	0.80[ASN][1000 genomes]
rs11965540	0.80[ASN][1000 genomes]
rs11967911	0.98[ASN][1000 genomes]
rs11968367	0.86[ASN][1000 genomes]
rs11968434	0.86[ASN][1000 genomes]
rs1264694	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264696	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1264702	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12661731	0.91[ASN][1000 genomes]
rs12663534	0.81[ASN][1000 genomes]
rs17187791	0.98[ASN][1000 genomes]
rs17187805	0.98[ASN][1000 genomes]
rs17194146	0.89[ASN][1000 genomes]
rs17194153	0.98[ASN][1000 genomes]
rs17194160	0.98[ASN][1000 genomes]
rs17194174	0.98[ASN][1000 genomes]
rs2072110	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240071	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2248289	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2285805	0.80[ASN][1000 genomes]
rs2394735	0.81[ASN][1000 genomes]
rs2523994	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844796	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28454792	0.96[ASN][1000 genomes]
rs28771211	0.82[ASN][1000 genomes]
rs28780078	0.91[ASN][1000 genomes]
rs28780079	0.91[ASN][1000 genomes]
rs28780080	0.91[ASN][1000 genomes]
rs28780081	0.91[ASN][1000 genomes]
rs28780082	0.90[ASN][1000 genomes]
rs3188482	0.80[ASN][1000 genomes]
rs3807032	0.81[ASN][1000 genomes]
rs3807033	0.81[ASN][1000 genomes]
rs57195817	0.84[ASN][1000 genomes]
rs57518619	0.81[ASN][1000 genomes]
rs58099508	0.81[ASN][1000 genomes]
rs60418878	0.85[ASN][1000 genomes]
rs61666432	0.86[ASN][1000 genomes]
rs6457149	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73424274	0.85[ASN][1000 genomes]
rs73728107	0.80[ASN][1000 genomes]
rs7741418	0.91[ASN][1000 genomes]
rs7749793	0.98[ASN][1000 genomes]
rs7753935	0.98[ASN][1000 genomes]
rs7754005	0.98[ASN][1000 genomes]
rs7761563	0.91[ASN][1000 genomes]
rs7765810	0.91[ASN][1000 genomes]
rs7771071	0.86[ASN][1000 genomes]
rs916569	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916570	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261384	0.91[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	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv884053	chr6:30059592-30070538	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1108053	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1108053	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1108053	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30068000-30072600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:30068200-30070200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:30068200-30071800	Flanking Active TSS	NHEK	skin
4	chr6:30068400-30070000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:30068400-30070000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:30068400-30070200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:30068400-30070200	Flanking Active TSS	HMEC	breast
8	chr6:30068400-30070400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
9	chr6:30068400-30071200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:30068600-30070000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:30068600-30070200	Active TSS	Aorta	Aorta
12	chr6:30068600-30070400	Flanking Active TSS	Left Ventricle	heart
13	chr6:30068600-30071600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr6:30068800-30070000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
15	chr6:30069000-30070000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:30069000-30070000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:30069000-30070600	Enhancers	Small Intestine	intestine
18	chr6:30069000-30071800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr6:30069200-30070000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
20	chr6:30069200-30070000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
21	chr6:30069200-30070000	Flanking Bivalent TSS/Enh	NH-A	brain
22	chr6:30069200-30070200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:30069200-30070200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
24	chr6:30069200-30070800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:30069400-30070200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
26	chr6:30069400-30070200	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr6:30069400-30070200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr6:30069400-30070200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
29	chr6:30069400-30070200	Flanking Active TSS	Placenta	Placenta
30	chr6:30069400-30070200	Flanking Active TSS	HSMM	muscle
31	chr6:30069400-30070200	Active TSS	HSMMtube	muscle
32	chr6:30069400-30070400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr6:30069400-30070400	Flanking Active TSS	Fetal Intestine Large	intestine
34	chr6:30069400-30070400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
35	chr6:30069400-30070400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr6:30069400-30070400	Bivalent/Poised TSS	HepG2	liver
37	chr6:30069400-30071000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr6:30069400-30071000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr6:30069400-30071000	Flanking Active TSS	Osteobl	bone
40	chr6:30069400-30071400	Active TSS	Esophagus	oesophagus
41	chr6:30069400-30071600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
42	chr6:30069400-30071800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
43	chr6:30069600-30070000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:30069600-30070000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:30069600-30070000	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr6:30069600-30070000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr6:30069600-30070000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:30069600-30070000	Bivalent Enhancer	Fetal Brain Male	brain
49	chr6:30069600-30070000	Flanking Active TSS	Spleen	Spleen
50	chr6:30069600-30070000	Active TSS	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links