Variant report

Variant	rs2072110
Chromosome Location	chr6:30070178-30070179
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	POLR2A	chr6:30069591-30070198	U87	brain:	n/a	n/a
2	BHLHE40	chr6:30069741-30070243	HepG2	liver:	n/a	n/a
3	NFIC	chr6:30069606-30070314	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:30069481-30070354	U87	brain:	n/a	n/a
5	ELF1	chr6:30069608-30070396	MCF-7	breast:	n/a	chr6:30070338-30070350 chr6:30070004-30070016
6	MAX	chr6:30069467-30070279	A549	lung:	n/a	n/a
7	POLR2A	chr6:30069631-30070216	HEK293	kidney:	n/a	n/a
8	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
9	CHD1	chr6:30070014-30070237	H1-hESC	embryonic stem cell:	n/a	n/a
10	JUND	chr6:30069975-30070251	H1-hESC	embryonic stem cell:	n/a	chr6:30070034-30070045
11	PML	chr6:30069579-30070183	MCF-7	breast:	n/a	n/a
12	POLR2A	chr6:30069647-30070182	K562	blood:	n/a	n/a
13	CEBPB	chr6:30069836-30070575	Hela-S3	cervix:	n/a	chr6:30070376-30070389 chr6:30070376-30070387
14	POLR2A	chr6:30069631-30070481	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr6:30069676-30070191	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr6:30068376-30071409	HepG2	liver:	n/a	n/a
17	ELF1	chr6:30069621-30070224	MCF-7	breast:	n/a	chr6:30070004-30070016
18	POLR2A	chr6:30069584-30070225	HCT-116	colon:	n/a	n/a
19	MAX	chr6:30069249-30070522	Hela-S3	cervix:	n/a	chr6:30069316-30069323 chr6:30069315-30069324
20	POLR2A	chr6:30069522-30070303	PFSK-1	brain:	n/a	n/a
21	MAX	chr6:30067884-30071564	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
22	JUND	chr6:30069701-30070185	HepG2	liver:	n/a	chr6:30070034-30070045
23	RAD21	chr6:30069651-30070213	MCF-7	breast:	n/a	chr6:30069746-30069765
24	POLR2A	chr6:30069547-30070410	SK-N-MC	brain:	n/a	n/a
25	POLR2A	chr6:30068290-30071350	HepG2	liver:	n/a	n/a
26	MYBL2	chr6:30068021-30071300	HepG2	liver:	n/a	n/a
27	NFIC	chr6:30069578-30070350	HepG2	liver:	n/a	n/a
28	MAX	chr6:30069578-30070245	A549	lung:	n/a	n/a
29	HMGN3	chr6:30069734-30070194	K562	blood:	n/a	n/a
30	MBD4	chr6:30069260-30070283	HepG2	liver:	n/a	n/a
31	RAD21	chr6:30069743-30070195	H1-hESC	embryonic stem cell:	n/a	chr6:30069746-30069765
32	FOSL2	chr6:30069600-30070225	HepG2	liver:	n/a	chr6:30070034-30070045
33	CEBPB	chr6:30070056-30070557	HepG2	liver:	n/a	chr6:30070376-30070389 chr6:30070376-30070387
34	RCOR1	chr6:30069558-30070214	K562	blood:	n/a	n/a
35	MYBL2	chr6:30069199-30070292	HepG2	liver:	n/a	n/a
36	MAZ	chr6:30069773-30070246	HepG2	liver:	n/a	n/a
37	POLR2A	chr6:30069556-30070187	A549	lung:	n/a	n/a
38	MAX	chr6:30068260-30070212	MCF-7	breast:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
39	ELF1	chr6:30069661-30070197	GM12878	blood:	n/a	chr6:30070004-30070016
40	TAF1	chr6:30069478-30070242	HepG2	liver:	n/a	n/a
41	POLR2A	chr6:30069604-30070237	HepG2	liver:	n/a	n/a
42	POLR2A	chr6:30069003-30070273	HepG2	liver:	n/a	n/a
43	CREB1	chr6:30068194-30071311	HepG2	liver:	n/a	n/a
44	POLR2A	chr6:30069659-30070217	A549	lung:	n/a	n/a
45	POLR2A	chr6:30069635-30070235	HepG2	liver:	n/a	n/a
46	POLR2A	chr6:30069362-30070411	PFSK-1	brain:	n/a	n/a
47	HDAC2	chr6:30069501-30070485	HepG2	liver:	n/a	chr6:30069635-30069649
48	POLR2A	chr6:30069480-30070396	Hela-S3	cervix:	n/a	n/a
49	HEY1	chr6:30069578-30070198	HepG2	liver:	n/a	chr6:30070002-30070017 chr6:30069966-30069981
50	ELK1	chr6:30069797-30070199	Hela-S3	cervix:	n/a	n/a

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	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
12	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
13	chr6:30027986..30030809-chr6:30067690..30071011,4	K562	blood:
14	chr18:12947541..12948216-chr6:30069780..30070632,2	Hela-S3	cervix:
15	chr6:30028086..30030535-chr6:30068315..30071049,3	MCF-7	breast:
16	chr6:30069286..30070342-chr6:30364378..30364933,3	K562	blood:
17	chr6:30042922..30044278-chr6:30069878..30071198,4	MCF-7	breast:
18	chr3:9438250..9438950-chr6:30069636..30070479,2	Hela-S3	cervix:
19	chr6:30024946..30027912-chr6:30068442..30070614,2	MCF-7	breast:
20	chr6:30068547..30070487-chr6:30073986..30076858,2	K562	blood:
21	chr6:30054838..30057804-chr6:30069131..30071158,2	MCF-7	breast:
22	chr6:30046314..30047956-chr6:30068316..30070912,2	MCF-7	breast:
23	chr6:29944151..29946628-chr6:30070054..30072125,2	K562	blood:

Variant related genes	Relation type
TRIM31-AS1	TF binding region
ENSG00000166224	Chromatin interaction
ENSG00000204619	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000227036	Chromatin interaction
ENSG00000204625	Chromatin interaction
ENSG00000166913	Chromatin interaction
ENSG00000252901	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000204610	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000204616	Chromatin interaction
ENSG00000066379	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	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1108053	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1110446	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1110448	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[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	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1264695	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1264696	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1264702	0.96[AFR][1000 genomes];0.95[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]
rs2240071	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2248289	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2523994	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844796	0.85[AMR][1000 genomes];0.90[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	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[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	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs916570	0.83[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
rs2072110	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2072110	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2072110	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 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	chr6:30068400-30070200	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr6:30068400-30070200	Flanking Active TSS	HMEC	breast
6	chr6:30068400-30070400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr6:30068400-30071200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:30068600-30070200	Active TSS	Aorta	Aorta
9	chr6:30068600-30070400	Flanking Active TSS	Left Ventricle	heart
10	chr6:30068600-30071600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr6:30069000-30070600	Enhancers	Small Intestine	intestine
12	chr6:30069000-30071800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:30069200-30070200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:30069200-30070200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
15	chr6:30069200-30070800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:30069400-30070200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
17	chr6:30069400-30070200	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr6:30069400-30070200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr6:30069400-30070200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
20	chr6:30069400-30070200	Flanking Active TSS	Placenta	Placenta
21	chr6:30069400-30070200	Flanking Active TSS	HSMM	muscle
22	chr6:30069400-30070200	Active TSS	HSMMtube	muscle
23	chr6:30069400-30070400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr6:30069400-30070400	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr6:30069400-30070400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
26	chr6:30069400-30070400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr6:30069400-30070400	Bivalent/Poised TSS	HepG2	liver
28	chr6:30069400-30071000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr6:30069400-30071000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr6:30069400-30071000	Flanking Active TSS	Osteobl	bone
31	chr6:30069400-30071400	Active TSS	Esophagus	oesophagus
32	chr6:30069400-30071600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
33	chr6:30069400-30071800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
34	chr6:30069600-30070200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:30069600-30070200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
36	chr6:30069600-30070200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr6:30069600-30070200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
38	chr6:30069600-30070200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:30069600-30070200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:30069600-30070200	Active TSS	Brain Angular Gyrus	brain
41	chr6:30069600-30070200	Active TSS	Colonic Mucosa	Colon
42	chr6:30069600-30070200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr6:30069600-30070200	Active TSS	Right Atrium	heart
44	chr6:30069600-30070200	Active TSS	Hela-S3	cervix
45	chr6:30069600-30070200	Flanking Active TSS	HUVEC	blood vessel
46	chr6:30069600-30070200	Active TSS	NHLF	lung
47	chr6:30069600-30070400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr6:30069600-30070400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
49	chr6:30069600-30070400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
50	chr6:30069600-30070400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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