Variant report

Variant	rs2294333
Chromosome Location	chr6:166756354-166756355
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	ZBTB7A	chr6:166755655-166756597	K562	blood:	n/a	n/a
2	POLR2A	chr6:166755780-166756396	U87	brain:	n/a	n/a
3	RELA	chr6:166755144-166757094	GM10847	blood:	n/a	n/a
4	MAX	chr6:166755825-166756361	MCF-7	breast:	n/a	n/a
5	SPI1	chr6:166756333-166757296	GM12878	blood:	n/a	chr6:166756809-166756822 chr6:166756812-166756821 chr6:166756810-166756823
6	POLR2A	chr6:166754998-166757076	HL-60	blood:	n/a	n/a
7	MBD4	chr6:166755841-166756635	HepG2	liver:	n/a	n/a
8	POLR2A	chr6:166755473-166757367	K562	blood:	n/a	n/a
9	TAF1	chr6:166755757-166756692	ECC-1	luminal epithelium:	n/a	n/a
10	EP300	chr6:166755857-166756903	GM12878	blood:	n/a	chr6:166756097-166756106
11	TAF1	chr6:166755696-166756787	GM12878	blood:	n/a	n/a
12	MYC	chr6:166755667-166756490	MCF10A-Er-Src	breast:	n/a	chr6:166755809-166755819
13	GTF2F1	chr6:166755590-166756792	K562	blood:	n/a	n/a
14	MAX	chr6:166755884-166756954	GM12878	blood:	n/a	n/a
15	ELK1	chr6:166755923-166756756	K562	blood:	n/a	n/a
16	TBP	chr6:166755843-166756417	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr6:166755470-166757207	GM18526	blood:	n/a	n/a
18	MAZ	chr6:166755668-166756798	HepG2	liver:	n/a	chr6:166755809-166755819
19	ETS1	chr6:166755694-166756451	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:166755788-166756602	HepG2	liver:	n/a	n/a
21	REST	chr6:166755813-166756434	A549	lung:	n/a	n/a
22	YY1	chr6:166755753-166756925	GM12878	blood:	n/a	n/a
23	NRF1	chr6:166755648-166757017	SK-N-SH	brain:	n/a	chr6:166756112-166756126 chr6:166756114-166756125 chr6:166756115-166756129 chr6:166756115-166756126
24	GABPA	chr6:166755763-166756490	HepG2	liver:	n/a	chr6:166756112-166756126 chr6:166756115-166756129 chr6:166756115-166756126
25	MAX	chr6:166755678-166756749	ECC-1	luminal epithelium:	n/a	chr6:166755809-166755819
26	GABPA	chr6:166755671-166756366	A549	lung:	n/a	chr6:166756112-166756126 chr6:166756115-166756129 chr6:166756115-166756126
27	POLR2A	chr6:166755379-166756958	GM12891	blood:	n/a	n/a
28	ZNF384	chr6:166756043-166756430	K562	blood:	n/a	n/a
29	ELF1	chr6:166755686-166756535	SK-N-SH	brain:	n/a	n/a
30	HEY1	chr6:166755379-166756658	K562	blood:	n/a	chr6:166755859-166755874
31	TCF12	chr6:166755736-166756447	ECC-1	luminal epithelium:	n/a	n/a
32	TCF12	chr6:166755603-166756455	ECC-1	luminal epithelium:	n/a	n/a
33	ELF1	chr6:166755709-166756461	HepG2	liver:	n/a	n/a
34	ZMIZ1	chr6:166755602-166756666	K562	blood:	n/a	n/a
35	POLR2A	chr6:166755446-166756921	GM19193	blood:	n/a	n/a
36	SIN3AK20	chr6:166755805-166756605	PANC-1	pancreas:	n/a	n/a
37	POLR2A	chr6:166755659-166756556	Hela-S3	cervix:	n/a	n/a
38	CREB1	chr6:166755673-166756859	HepG2	liver:	n/a	n/a
39	HEY1	chr6:166755845-166756645	HepG2	liver:	n/a	chr6:166755859-166755874
40	TEAD4	chr6:166755836-166757023	K562	blood:	n/a	n/a
41	POLR2A	chr6:166755072-166758044	K562	blood:	n/a	n/a
42	POLR2A	chr6:166755808-166756517	H1-hESC	embryonic stem cell:	n/a	n/a
43	PAX5	chr6:166755701-166756771	GM12878	blood:	n/a	chr6:166756095-166756104
44	PML	chr6:166755716-166757050	K562	blood:	n/a	n/a
45	EGR1	chr6:166755857-166756421	GM12878	blood:	n/a	chr6:166756116-166756125
46	RELA	chr6:166755584-166756885	GM18526	blood:	n/a	n/a
47	UBTF	chr6:166755809-166756716	K562	blood:	n/a	n/a
48	MTA3	chr6:166754882-166757246	GM12878	blood:	n/a	n/a
49	ZNF143	chr6:166755923-166756497	Hela-S3	cervix:	n/a	n/a
50	YY1	chr6:166755714-166756516	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:56708892..56709643-chr6:166755874..166756473,2	NB4	blood:
2	chr6:166751804..166757558-chr6:166793969..166799153,5	K562	blood:
3	chr1:90460546..90461351-chr6:166756027..166757000,2	NB4	blood:
4	chr6:166755930..166757619-chr6:166781019..166784045,3	MCF-7	breast:
5	chr6:166754173..166757774-chr6:166795355..166798060,3	MCF-7	breast:
6	chr6:166753320..166757958-chr6:166794622..166799153,8	K562	blood:
7	chr1:16161823..16162608-chr6:166755664..166756528,2	Hela-S3	cervix:
8	chr6:166719852..166722547-chr6:166755922..166758056,2	K562	blood:
9	chr6:166756132..166758070-chr6:166759956..166762577,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGFR1OP-3	chr6:166756132-166756635	ENSG00000232468
2	lnc-FGFR1OP-3	chr6:166756030-166756617	NONHSAT116042
3	lnc-FGFR1OP-3	chr6:166756119-166756635	NONHSAT116043

Variant related genes	Relation type
SFT2D1	TF binding region
ENSG00000212195	Chromatin interaction
ENSG00000179743	Chromatin interaction
ENSG00000162664	Chromatin interaction
ENSG00000176381	Chromatin interaction
ENSG00000060762	Chromatin interaction
ENSG00000261420	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10455809	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10455976	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10455977	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10455978	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10946152	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10946158	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10946160	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10946161	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11551053	0.89[ASN][1000 genomes]
rs11752886	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11753652	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11755305	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12198613	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209616	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12214281	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12214812	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12662924	0.84[EUR][1000 genomes]
rs1599841	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294335	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4144886	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144887	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144888	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55936781	0.83[EUR][1000 genomes]
rs59337176	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66461381	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68016351	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73030701	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73263155	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73788236	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7740965	0.81[AMR][1000 genomes]
rs7753161	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7767887	0.83[ASN][1000 genomes]
rs7771603	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941683	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
2	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2294333	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166754600-166756600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:166754600-166756600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:166754600-166756800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:166754600-166756800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr6:166754600-166756800	Active TSS	GM12878-XiMat	blood
6	chr6:166754800-166756400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:166754800-166756600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:166754800-166756600	Active TSS	Hela-S3	cervix
9	chr6:166754800-166757000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr6:166754800-166757000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:166754800-166757000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:166754800-166757000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:166754800-166757000	Active TSS	Colonic Mucosa	Colon
14	chr6:166754800-166757200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:166755000-166756400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr6:166755000-166756600	Active TSS	Aorta	Aorta
17	chr6:166755000-166756600	Active TSS	Brain Substantia Nigra	brain
18	chr6:166755000-166756800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:166755000-166756800	Active TSS	H9 Cell Line	embryonic stem cell
20	chr6:166755000-166756800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:166755000-166756800	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr6:166755000-166756800	Active TSS	Lung	lung
23	chr6:166755000-166756800	Active TSS	Ovary	ovary
24	chr6:166755000-166756800	Active TSS	Rectal Smooth Muscle	rectum
25	chr6:166755000-166756800	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr6:166755000-166756800	Active TSS	NHDF-Ad	bronchial
27	chr6:166755000-166757000	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr6:166755000-166757000	Active TSS	H1 Cell Line	embryonic stem cell
29	chr6:166755000-166757000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:166755000-166757000	Active TSS	Left Ventricle	heart
31	chr6:166755000-166757000	Active TSS	Psoas Muscle	Psoas
32	chr6:166755000-166757200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr6:166755000-166757200	Active TSS	A549	lung
34	chr6:166755000-166757200	Active TSS	NHLF	lung
35	chr6:166755200-166756400	Active TSS	Primary B cells from peripheral blood	blood
36	chr6:166755200-166756400	Active TSS	Primary T cells from cord blood	blood
37	chr6:166755200-166756400	Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr6:166755200-166756400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr6:166755200-166756400	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr6:166755200-166756400	Active TSS	Brain Hippocampus Middle	brain
41	chr6:166755200-166756400	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr6:166755200-166756600	Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr6:166755200-166756600	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr6:166755200-166756600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr6:166755200-166756600	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr6:166755200-166756600	Active TSS	Duodenum Mucosa	Duodenum
47	chr6:166755200-166756600	Active TSS	Esophagus	oesophagus
48	chr6:166755200-166756600	Active TSS	Fetal Intestine Small	intestine
49	chr6:166755200-166756600	Active TSS	Fetal Stomach	stomach
50	chr6:166755200-166756600	Active TSS	Placenta Amnion	Placenta Amnion

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