Variant report

Variant	rs2523994
Chromosome Location	chr6:30070346-30070347
allele	G/T
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	chr6:30069481-30070354	U87	brain:	n/a	n/a
2	ELF1	chr6:30069608-30070396	MCF-7	breast:	n/a	chr6:30070338-30070350 chr6:30070004-30070016
3	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
4	CEBPB	chr6:30069836-30070575	Hela-S3	cervix:	n/a	chr6:30070376-30070389 chr6:30070376-30070387
5	POLR2A	chr6:30069631-30070481	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr6:30070260-30070569	K562	blood:	n/a	chr6:30070376-30070389 chr6:30070376-30070387
7	POLR2A	chr6:30068376-30071409	HepG2	liver:	n/a	n/a
8	MAX	chr6:30069249-30070522	Hela-S3	cervix:	n/a	chr6:30069316-30069323 chr6:30069315-30069324
9	MYC	chr6:30070296-30070457	MCF10A-Er-Src	breast:	n/a	n/a
10	MAX	chr6:30067884-30071564	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
11	STAT3	chr6:30070329-30070495	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr6:30069547-30070410	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr6:30068290-30071350	HepG2	liver:	n/a	n/a
14	MYBL2	chr6:30068021-30071300	HepG2	liver:	n/a	n/a
15	NFIC	chr6:30069578-30070350	HepG2	liver:	n/a	n/a
16	CTCF	chr6:30070260-30070410	BJ	skin:	n/a	n/a
17	MBD4	chr6:30070259-30071149	HepG2	liver:	n/a	n/a
18	POLR2A	chr6:30070344-30070352	K562	blood:	n/a	n/a
19	CEBPB	chr6:30070056-30070557	HepG2	liver:	n/a	chr6:30070376-30070389 chr6:30070376-30070387
20	FOS	chr6:30070293-30070432	MCF10A-Er-Src	breast:	n/a	n/a
21	CREB1	chr6:30068194-30071311	HepG2	liver:	n/a	n/a
22	FOS	chr6:30070309-30070533	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr6:30069362-30070411	PFSK-1	brain:	n/a	n/a
24	HDAC2	chr6:30069501-30070485	HepG2	liver:	n/a	chr6:30069635-30069649
25	POLR2A	chr6:30069480-30070396	Hela-S3	cervix:	n/a	n/a
26	TEAD4	chr6:30070308-30071143	HepG2	liver:	n/a	n/a
27	FOS	chr6:30070315-30070510	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr6:30069487-30070348	U87	brain:	n/a	n/a
29	MAZ	chr6:30069160-30071487	IMR90	lung:	n/a	chr6:30069316-30069323 chr6:30069315-30069324
30	CEBPB	chr6:30070270-30070540	IMR90	lung:	n/a	chr6:30070376-30070389 chr6:30070376-30070387
31	CTCF	chr6:30070233-30071526	HCT-116	colon:	n/a	n/a
32	CEBPB	chr6:30070295-30070485	A549	lung:	n/a	chr6:30070376-30070389 chr6:30070376-30070387
33	RCOR1	chr6:30069557-30070467	Hela-S3	cervix:	n/a	n/a
34	MAX	chr6:30067993-30070449	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
35	SMARCC1	chr6:30069564-30071165	Hela-S3	cervix:	n/a	n/a
36	CTCF	chr6:30069267-30071939	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr6:30069590-30070481	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr6:30069638-30070501	MCF10A-Er-Src	breast:	n/a	n/a
39	E2F4	chr6:30069744-30070477	MCF10A-Er-Src	breast:	n/a	chr6:30069962-30069972 chr6:30069998-30070008 chr6:30069967-30069976
40	HEY1	chr6:30068212-30071230	HepG2	liver:	n/a	chr6:30070002-30070017 chr6:30069966-30069981
41	FOS	chr6:30070315-30070515	MCF10A-Er-Src	breast:	n/a	n/a
42	CTCF	chr6:30069586-30072183	A549	lung:	n/a	n/a
43	YY1	chr6:30069535-30070352	HepG2	liver:	n/a	chr6:30069998-30070012 chr6:30070003-30070012 chr6:30069967-30069976 chr6:30069965-30069979

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:30070342-30070392	HAEpiC	amniotic membrane:	n/a
2	chr6:30070342-30070392	AG04450	lung:	fetal
3	chr6:30070342-30070392	HCPEpiC	choroid plexus:	n/a
4	chr6:30070342-30070392	AoSMC	blood vessel:	n/a
5	chr6:30070342-30070392	HRCEpiC	kidney:	n/a
6	chr6:30070342-30070392	IMR90	lung:	fetal
7	chr6:30070342-30070392	SK-N-SH	brain:	n/a
8	chr6:30070342-30070392	SK-N-MC	brain:	n/a
9	chr6:30070342-30070392	A549	lung:	n/a
10	chr6:30070342-30070392	PrEC	prostate:	n/a
11	chr6:30070342-30070392	HMEC	breast:	n/a
12	chr6:30070342-30070392	GM06990	blood:	n/a
13	chr6:30070342-30070392	HEK293	kidney:	embryo
14	chr6:30070342-30070392	U87	brain:	n/a
15	chr6:30070342-30070392	SKMC	muscle:	n/a
16	chr6:30070342-30070392	GM12892	blood:	n/a
17	chr6:30070342-30070392	AG09319	gingival:	n/a
18	chr6:30070342-30070392	HUVEC	blood vessel:	n/a
19	chr6:30070342-30070392	ECC-1	luminal epithelium:	n/a
20	chr6:30070342-30070392	MCF10A-Er-Src	breast:	n/a
21	chr6:30070342-30070392	Jurkat	blood:	n/a
22	chr6:30070342-30070392	HRPEpiC	eye:	n/a
23	chr6:30070342-30070392	HNPCEpiC	eye:	n/a
24	chr6:30070342-30070392	NH-A	brain:	n/a
25	chr6:30070342-30070392	GM19239	blood:	n/a
26	chr6:30070342-30070392	HPAEpiC	pulmonary alveolar:	n/a
27	chr6:30070342-30070392	HRE	kidney:	n/a
28	chr6:30070342-30070392	NHBE	bronchial:	n/a
29	chr6:30070342-30070392	K562	blood:	n/a
30	chr6:30070342-30070392	HIPEpiC	eye:	n/a
31	chr6:30070342-30070392	ovcar-3	ovarian:	n/a
32	chr6:30070342-30070392	MCF-7	breast:	n/a
33	chr6:30070342-30070392	SK-N-SH_RA	brain:	n/a
34	chr6:30070342-30070392	LNCaP	prostate:	n/a
35	chr6:30070342-30070392	H1-hESC	embryonic stem cell:	embryo
36	chr6:30070342-30070392	BJ	skin:	n/a
37	chr6:30070342-30070392	NHDF-neo	bronchial:	n/a
38	chr6:30070342-30070392	Hepatocyte	liver:	n/a
39	chr6:30070342-30070392	GM12891	blood:	n/a
40	chr6:30070342-30070392	BE2_C	brain:	n/a
41	chr6:30070342-30070392	HL-60	blood:	n/a
42	chr6:30070342-30070392	SAEC	small airway:	n/a
43	chr6:30070342-30070392	PFSK-1	brain:	n/a
44	chr6:30070342-30070392	RPTEC	kidney:	n/a
45	chr6:30070342-30070392	HEEpiC	esophagus:	n/a
46	chr6:30070342-30070392	HCF	heart:	n/a
47	chr6:30070342-30070392	AG10803	skin:	n/a
48	chr6:30070342-30070392	HCT-116	colon:	n/a
49	chr6:30070342-30070392	ProgFib	skin:	n/a
50	chr6:30070342-30070392	AG09309	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30031338..30034907-chr6:30068673..30070684,4	MCF-7	breast:
2	chr6:30070301..30072986-chr6:30097734..30100221,43	MCF-7	breast:
3	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
4	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
5	chr6:30027872..30030809-chr6:30069511..30072907,4	K562	blood:
6	chr6:30069516..30071040-chr6:30137847..30139463,2	MCF-7	breast:
7	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
8	chr6:30070180..30072059-chr6:30098450..30099535,14	K562	blood:
9	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
10	chr6:30027986..30030809-chr6:30067690..30071011,4	K562	blood:
11	chr18:12947541..12948216-chr6:30069780..30070632,2	Hela-S3	cervix:
12	chr6:30028086..30030535-chr6:30068315..30071049,3	MCF-7	breast:
13	chr6:30043377..30045110-chr6:30070275..30072110,2	MCF-7	breast:
14	chr6:30042922..30044278-chr6:30069878..30071198,4	MCF-7	breast:
15	chr3:9438250..9438950-chr6:30069636..30070479,2	Hela-S3	cervix:
16	chr6:30024946..30027912-chr6:30068442..30070614,2	MCF-7	breast:
17	chr6:30068547..30070487-chr6:30073986..30076858,2	K562	blood:
18	chr6:30054838..30057804-chr6:30069131..30071158,2	MCF-7	breast:
19	chr6:30046314..30047956-chr6:30068316..30070912,2	MCF-7	breast:
20	chr6:29944151..29946628-chr6:30070054..30072125,2	K562	blood:

Variant related genes	Relation type
TRIM31-AS1	TF binding region
TRIM31-AS1	CpG island
ENSG00000234127	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000204619	Chromatin interaction
ENSG00000204625	Chromatin interaction
ENSG00000252901	Chromatin interaction
ENSG00000204616	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000204610	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1108052	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1108053	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1110446	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1110448	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1156533	0.89[ASN][1000 genomes]
rs11751554	0.84[ASN][1000 genomes]
rs11967911	0.95[ASN][1000 genomes]
rs11968367	0.84[ASN][1000 genomes]
rs11968434	0.84[ASN][1000 genomes]
rs1264694	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1264695	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1264696	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1264702	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12661731	0.89[ASN][1000 genomes]
rs17187791	0.95[ASN][1000 genomes]
rs17187805	0.95[ASN][1000 genomes]
rs17194146	0.87[ASN][1000 genomes]
rs17194153	0.95[ASN][1000 genomes]
rs17194160	0.95[ASN][1000 genomes]
rs17194174	0.95[ASN][1000 genomes]
rs2072110	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240071	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2248289	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2844796	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28454792	0.94[ASN][1000 genomes]
rs28771211	0.81[ASN][1000 genomes]
rs28780078	0.89[ASN][1000 genomes]
rs28780079	0.89[ASN][1000 genomes]
rs28780080	0.89[ASN][1000 genomes]
rs28780081	0.88[ASN][1000 genomes]
rs28780082	0.88[ASN][1000 genomes]
rs57195817	0.82[ASN][1000 genomes]
rs60418878	0.83[ASN][1000 genomes]
rs61666432	0.84[ASN][1000 genomes]
rs6457149	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73424274	0.83[ASN][1000 genomes]
rs7741418	0.89[ASN][1000 genomes]
rs7749793	0.95[ASN][1000 genomes]
rs7753935	0.95[ASN][1000 genomes]
rs7754005	0.95[ASN][1000 genomes]
rs7761563	0.89[ASN][1000 genomes]
rs7765810	0.89[ASN][1000 genomes]
rs7771071	0.84[ASN][1000 genomes]
rs916569	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs916570	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9261384	0.89[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
rs2523994	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2523994	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs2523994	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 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	chr6:30068200-30071800	Flanking Active TSS	NHEK	skin
3	chr6:30068400-30070400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
4	chr6:30068400-30071200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:30068600-30070400	Flanking Active TSS	Left Ventricle	heart
6	chr6:30068600-30071600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr6:30069000-30070600	Enhancers	Small Intestine	intestine
8	chr6:30069000-30071800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
9	chr6:30069200-30070800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:30069400-30070400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
11	chr6:30069400-30070400	Flanking Active TSS	Fetal Intestine Large	intestine
12	chr6:30069400-30070400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
13	chr6:30069400-30070400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr6:30069400-30070400	Bivalent/Poised TSS	HepG2	liver
15	chr6:30069400-30071000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr6:30069400-30071000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr6:30069400-30071000	Flanking Active TSS	Osteobl	bone
18	chr6:30069400-30071400	Active TSS	Esophagus	oesophagus
19	chr6:30069400-30071600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
20	chr6:30069400-30071800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
21	chr6:30069600-30070400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr6:30069600-30070400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr6:30069600-30070400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:30069600-30070400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:30069600-30070400	Active TSS	A549	lung
26	chr6:30069600-30070600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
27	chr6:30069600-30071000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
28	chr6:30069600-30071200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:30069600-30071200	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr6:30069600-30071400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:30069600-30071400	Active TSS	Psoas Muscle	Psoas
32	chr6:30069600-30071600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr6:30069800-30070400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
34	chr6:30069800-30070400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:30069800-30070400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:30069800-30070400	Active TSS	Colon Smooth Muscle	Colon
37	chr6:30069800-30070600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:30069800-30070800	Active TSS	Brain Inferior Temporal Lobe	brain
39	chr6:30069800-30070800	Active TSS	Fetal Kidney	kidney
40	chr6:30069800-30071000	Enhancers	Stomach Mucosa	stomach
41	chr6:30069800-30071000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr6:30069800-30071200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr6:30069800-30071200	Active TSS	Brain Anterior Caudate	brain
44	chr6:30069800-30071200	Active TSS	Brain Substantia Nigra	brain
45	chr6:30069800-30071200	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr6:30069800-30071800	Active TSS	Rectal Smooth Muscle	rectum
47	chr6:30070000-30070400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:30070000-30070400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:30070000-30070400	Flanking Active TSS	Liver	Liver
50	chr6:30070000-30070400	Flanking Active TSS	Brain Cingulate Gyrus	brain

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