Variant report

Variant	rs1108052
Chromosome Location	chr6:30069795-30069796
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:239)
CpG islands
(count:61)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:239 , 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	chr6:30069720-30069870	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	POLR2A	chr6:30069597-30070082	Gliobla	brain:	n/a	n/a
9	POLR2A	chr6:30069481-30070354	U87	brain:	n/a	n/a
10	POLR2A	chr6:30069578-30070070	SK-N-MC	brain:	n/a	n/a
11	CTCF	chr6:30069738-30069954	GM19238	blood:	n/a	n/a
12	CTCF	chr6:30069780-30069930	AG10803	skin:	n/a	n/a
13	CTCF	chr6:30069720-30069870	SAEC	small airway:	n/a	n/a
14	ELF1	chr6:30069608-30070396	MCF-7	breast:	n/a	chr6:30070338-30070350 chr6:30070004-30070016
15	ELF1	chr6:30069697-30070148	K562	blood:	n/a	chr6:30070004-30070016
16	MAX	chr6:30069467-30070279	A549	lung:	n/a	n/a
17	CTCF	chr6:30069772-30069943	HepG2	liver:	n/a	n/a
18	POLR2A	chr6:30069661-30069923	H1-hESC	embryonic stem cell:	n/a	n/a
19	CEBPD	chr6:30069675-30069992	HepG2	liver:	n/a	n/a
20	POLR2A	chr6:30069631-30070216	HEK293	kidney:	n/a	n/a
21	CTCF	chr6:30069733-30069933	GM19240	blood:	n/a	n/a
22	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
23	CTCF	chr6:30069760-30069910	HCFaa	heart:	n/a	n/a
24	CTCF	chr6:30069700-30069850	HEEpiC	esophagus:	n/a	n/a
25	CTCF	chr6:30069780-30069930	GM12870	blood:	n/a	n/a
26	CTCF	chr6:30069780-30069930	WERI-Rb-1	eye:	n/a	n/a
27	CTCF	chr6:30069780-30069930	HPAF	blood vessel:	n/a	n/a
28	CTCF	chr6:30069771-30069932	NHEK	skin:	n/a	n/a
29	CTCF	chr6:30069660-30069810	HFF	foreskin:	n/a	n/a
30	CTCF	chr6:30069780-30069930	SK-N-SH_RA	brain:	n/a	n/a
31	MXI1	chr6:30069677-30070146	HepG2	liver:	n/a	n/a
32	SIN3A	chr6:30069652-30070124	H1-hESC	embryonic stem cell:	n/a	n/a
33	PML	chr6:30069579-30070183	MCF-7	breast:	n/a	n/a
34	MXI1	chr6:30069752-30069860	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:30069647-30070182	K562	blood:	n/a	n/a
36	MAZ	chr6:30069697-30070100	K562	blood:	n/a	n/a
37	CTCF	chr6:30069720-30069870	HCM	heart:	n/a	n/a
38	POLR2A	chr6:30069631-30070481	MCF10A-Er-Src	breast:	n/a	n/a
39	MAX	chr6:30069191-30069933	H1-hESC	embryonic stem cell:	n/a	chr6:30069316-30069323 chr6:30069315-30069324
40	ZNF263	chr6:30069497-30070070	HEK293-T-REx	kidney:	n/a	chr6:30069717-30069738
41	CTCF	chr6:30069769-30069958	A549	lung:	n/a	n/a
42	CTCF	chr6:30069710-30069943	Fibrobl	skin:	n/a	n/a
43	CTCF	chr6:30069772-30069953	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr6:30069760-30069910	HCPEpiC	choroid plexus:	n/a	n/a
45	CTCF	chr6:30069680-30069830	GM12866	blood:	n/a	n/a
46	POLR2A	chr6:30069676-30070191	Hela-S3	cervix:	n/a	n/a
47	CEBPD	chr6:30069671-30070175	HepG2	liver:	n/a	n/a
48	CTCF	chr6:30069780-30069930	HepG2	liver:	n/a	n/a
49	POLR2A	chr6:30068376-30071409	HepG2	liver:	n/a	n/a
50	ELF1	chr6:30069621-30070224	MCF-7	breast:	n/a	chr6:30070004-30070016

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30069780-30069830	HUVEC	blood vessel:	n/a
2	chr6:30069780-30069830	HMEC	breast:	n/a
3	chr6:30069780-30069830	HPAEpiC	pulmonary alveolar:	n/a
4	chr6:30069780-30069830	GM12878	blood:	n/a
5	chr6:30069780-30069830	NHDF-neo	bronchial:	n/a
6	chr6:30069780-30069830	K562	blood:	n/a
7	chr6:30069780-30069830	HAEpiC	amniotic membrane:	n/a
8	chr6:30069780-30069830	PrEC	prostate:	n/a
9	chr6:30069780-30069830	HNPCEpiC	eye:	n/a
10	chr6:30069780-30069830	GM19239	blood:	n/a
11	chr6:30069780-30069830	AoSMC	blood vessel:	n/a
12	chr6:30069780-30069830	LNCaP	prostate:	n/a
13	chr6:30069780-30069830	Caco-2	colon:	n/a
14	chr6:30069780-30069830	BJ	skin:	n/a
15	chr6:30069780-30069830	HRPEpiC	eye:	n/a
16	chr6:30069780-30069830	SAEC	small airway:	n/a
17	chr6:30069780-30069830	ProgFib	skin:	n/a
18	chr6:30069780-30069830	T-47D	breast:	n/a
19	chr6:30069780-30069830	CMK	blood:	n/a
20	chr6:30069780-30069830	HCT-116	colon:	n/a
21	chr6:30069780-30069830	HCF	heart:	n/a
22	chr6:30069780-30069830	H1-hESC	embryonic stem cell:	embryo
23	chr6:30069780-30069830	HEEpiC	esophagus:	n/a
24	chr6:30069780-30069830	SKMC	muscle:	n/a
25	chr6:30069780-30069830	HepG2	liver:	n/a
26	chr6:30069780-30069830	Jurkat	blood:	n/a
27	chr6:30069780-30069830	ECC-1	luminal epithelium:	n/a
28	chr6:30069780-30069830	U87	brain:	n/a
29	chr6:30069780-30069830	GM12892	blood:	n/a
30	chr6:30069780-30069830	NT2-D1	testis:	n/a
31	chr6:30069780-30069830	BE2_C	brain:	n/a
32	chr6:30069780-30069830	MCF-7	breast:	n/a
33	chr6:30069780-30069830	A549	lung:	n/a
34	chr6:30069780-30069830	SK-N-SH_RA	brain:	n/a
35	chr6:30069780-30069830	IMR90	lung:	fetal
36	chr6:30069780-30069830	PANC-1	pancreas:	n/a
37	chr6:30069780-30069830	RPTEC	kidney:	n/a
38	chr6:30069780-30069830	PFSK-1	brain:	n/a
39	chr6:30069780-30069830	ovcar-3	ovarian:	n/a
40	chr6:30069780-30069830	NHBE	bronchial:	n/a
41	chr6:30069780-30069830	AG04450	lung:	fetal
42	chr6:30069780-30069830	AG10803	skin:	n/a
43	chr6:30069780-30069830	NB4	blood:	n/a
44	chr6:30069780-30069830	HRE	kidney:	n/a
45	chr6:30069780-30069830	NH-A	brain:	n/a
46	chr6:30069780-30069830	Hepatocyte	liver:	n/a
47	chr6:30069780-30069830	MCF10A-Er-Src	breast:	n/a
48	chr6:30069780-30069830	SK-N-SH	brain:	n/a
49	chr6:30069780-30069830	HL-60	blood:	n/a
50	chr6:30069780-30069830	GM06990	blood:	n/a

(count:30 , 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	chr6:30004933..30007814-chr6:30068168..30069816,2	MCF-7	breast:
14	chr17:73720378..73720925-chr6:30069323..30069983,2	HCT-116	colon:
15	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
16	chr6:30027986..30030809-chr6:30067690..30071011,4	K562	blood:
17	chr6:30059663..30061808-chr6:30067229..30070058,2	K562	blood:
18	chr18:12947541..12948216-chr6:30069780..30070632,2	Hela-S3	cervix:
19	chr6:30028086..30030535-chr6:30068315..30071049,3	MCF-7	breast:
20	chr6:30067195..30070112-chr6:30098151..30100617,2	MCF-7	breast:
21	chr6:30069286..30070342-chr6:30364378..30364933,3	K562	blood:
22	chr3:9438250..9438950-chr6:30069636..30070479,2	Hela-S3	cervix:
23	chr6:30039276..30042217-chr6:30067253..30069841,2	K562	blood:
24	chr6:30024946..30027912-chr6:30068442..30070614,2	MCF-7	breast:
25	chr6:30068547..30070487-chr6:30073986..30076858,2	K562	blood:
26	chr6:30063791..30066840-chr6:30067476..30070156,3	MCF-7	breast:
27	chr6:30034219..30034740-chr6:30069488..30070083,2	Hela-S3	cervix:
28	chr6:30067592..30070049-chr6:30312859..30314391,2	K562	blood:
29	chr6:30054838..30057804-chr6:30069131..30071158,2	MCF-7	breast:
30	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
ENSG00000204616	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000166224	Chromatin interaction
ENSG00000204619	Chromatin interaction
ENSG00000227036	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000166913	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000132470	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000252901	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000204614	Chromatin interaction
ENSG00000204610	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1108053	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]
rs1110448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1156533	0.88[ASN][1000 genomes]
rs11751554	0.83[ASN][1000 genomes]
rs11967911	0.94[ASN][1000 genomes]
rs11968367	0.83[ASN][1000 genomes]
rs11968434	0.83[ASN][1000 genomes]
rs1264694	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1264695	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264696	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264702	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12661731	0.88[ASN][1000 genomes]
rs17187791	0.94[ASN][1000 genomes]
rs17187805	0.94[ASN][1000 genomes]
rs17194146	0.86[ASN][1000 genomes]
rs17194153	0.94[ASN][1000 genomes]
rs17194160	0.94[ASN][1000 genomes]
rs17194174	0.94[ASN][1000 genomes]
rs2072110	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2240071	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2248289	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2523994	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2524005	1.00[CEU][hapmap]
rs2844796	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28454792	0.93[ASN][1000 genomes]
rs28780078	0.88[ASN][1000 genomes]
rs28780079	0.88[ASN][1000 genomes]
rs28780080	0.88[ASN][1000 genomes]
rs28780081	0.87[ASN][1000 genomes]
rs28780082	0.86[ASN][1000 genomes]
rs57195817	0.81[ASN][1000 genomes]
rs60418878	0.82[ASN][1000 genomes]
rs61666432	0.83[ASN][1000 genomes]
rs6457149	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73424274	0.82[ASN][1000 genomes]
rs7741418	0.88[ASN][1000 genomes]
rs7749793	0.94[ASN][1000 genomes]
rs7753935	0.94[ASN][1000 genomes]
rs7754005	0.94[ASN][1000 genomes]
rs7761563	0.88[ASN][1000 genomes]
rs7765810	0.88[ASN][1000 genomes]
rs7771071	0.83[ASN][1000 genomes]
rs916569	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs916570	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9261384	0.88[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs1108052	ZSCAN23	cis	parietal	SCAN
rs1108052	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs1108052	BTN3A2	cis	parietal	SCAN
rs1108052	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1108052	ZNF323	cis	parietal	SCAN
rs1108052	HIST1H2AM	cis	parietal	SCAN
rs1108052	ABT1	cis	parietal	SCAN
rs1108052	HIST1H2BM	cis	cerebellum	SCAN
rs1108052	ZNRD1	cis	lymphoblastoid	seeQTL
rs1108052	ZKSCAN3	cis	parietal	SCAN
rs1108052	HIST1H4G	cis	cerebellum	SCAN
rs1108052	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1108052	HIST1H2BN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30068000-30069800	Enhancers	Lung	lung
2	chr6:30068000-30072600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:30068200-30069800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:30068200-30069800	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr6:30068200-30070200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:30068200-30071800	Flanking Active TSS	NHEK	skin
7	chr6:30068400-30069800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
8	chr6:30068400-30069800	Flanking Active TSS	Pancreas	Pancrea
9	chr6:30068400-30069800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
10	chr6:30068400-30069800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
11	chr6:30068400-30069800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr6:30068400-30070000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:30068400-30070000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
14	chr6:30068400-30070200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:30068400-30070200	Flanking Active TSS	HMEC	breast
16	chr6:30068400-30070400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr6:30068400-30071200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:30068600-30069800	Flanking Bivalent TSS/Enh	Thymus	Thymus
19	chr6:30068600-30070000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:30068600-30070200	Active TSS	Aorta	Aorta
21	chr6:30068600-30070400	Flanking Active TSS	Left Ventricle	heart
22	chr6:30068600-30071600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr6:30068800-30069800	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
24	chr6:30068800-30069800	Flanking Active TSS	Right Ventricle	heart
25	chr6:30068800-30069800	Flanking Active TSS	Stomach Mucosa	stomach
26	chr6:30068800-30070000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
27	chr6:30069000-30069800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
28	chr6:30069000-30069800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:30069000-30069800	Flanking Active TSS	Liver	Liver
30	chr6:30069000-30069800	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
31	chr6:30069000-30070000	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:30069000-30070000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:30069000-30070600	Enhancers	Small Intestine	intestine
34	chr6:30069000-30071800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr6:30069200-30069800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr6:30069200-30069800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
37	chr6:30069200-30069800	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:30069200-30069800	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
39	chr6:30069200-30069800	Flanking Active TSS	Ovary	ovary
40	chr6:30069200-30070000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:30069200-30070000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
42	chr6:30069200-30070000	Flanking Bivalent TSS/Enh	NH-A	brain
43	chr6:30069200-30070200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:30069200-30070200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
45	chr6:30069200-30070800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:30069400-30069800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
47	chr6:30069400-30069800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr6:30069400-30069800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:30069400-30069800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:30069400-30069800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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