Variant report

Variant	rs2294334
Chromosome Location	chr6:166756179-166756180
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:429)
CpG islands
(count:61)
Chromatin interactive
region (count:9)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:429 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

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	CREB1	chr6:166755920-166756208	A549	lung:	n/a	n/a
3	GTF2F1	chr6:166755963-166756301	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:166755780-166756396	U87	brain:	n/a	n/a
5	RELA	chr6:166755144-166757094	GM10847	blood:	n/a	n/a
6	MAX	chr6:166755825-166756361	MCF-7	breast:	n/a	n/a
7	POLR2A	chr6:166754998-166757076	HL-60	blood:	n/a	n/a
8	MBD4	chr6:166755841-166756635	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:166755473-166757367	K562	blood:	n/a	n/a
10	NFIC	chr6:166755756-166756348	GM12878	blood:	n/a	n/a
11	TAF1	chr6:166755757-166756692	ECC-1	luminal epithelium:	n/a	n/a
12	EP300	chr6:166755857-166756903	GM12878	blood:	n/a	chr6:166756097-166756106
13	TAF1	chr6:166755696-166756787	GM12878	blood:	n/a	n/a
14	MYC	chr6:166755667-166756490	MCF10A-Er-Src	breast:	n/a	chr6:166755809-166755819
15	GTF2F1	chr6:166755590-166756792	K562	blood:	n/a	n/a
16	MAX	chr6:166755884-166756954	GM12878	blood:	n/a	n/a
17	ELK1	chr6:166755923-166756756	K562	blood:	n/a	n/a
18	TBP	chr6:166755843-166756417	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr6:166755470-166757207	GM18526	blood:	n/a	n/a
20	MAZ	chr6:166755668-166756798	HepG2	liver:	n/a	chr6:166755809-166755819
21	ETS1	chr6:166755694-166756451	GM12878	blood:	n/a	n/a
22	MYC	chr6:166756062-166756293	K562	blood:	n/a	n/a
23	POLR2A	chr6:166755788-166756602	HepG2	liver:	n/a	n/a
24	REST	chr6:166755813-166756434	A549	lung:	n/a	n/a
25	YY1	chr6:166755753-166756925	GM12878	blood:	n/a	n/a
26	NRF1	chr6:166755648-166757017	SK-N-SH	brain:	n/a	chr6:166756112-166756126 chr6:166756114-166756125 chr6:166756115-166756129 chr6:166756115-166756126
27	GABPA	chr6:166755763-166756490	HepG2	liver:	n/a	chr6:166756112-166756126 chr6:166756115-166756129 chr6:166756115-166756126
28	MAX	chr6:166755678-166756749	ECC-1	luminal epithelium:	n/a	chr6:166755809-166755819
29	GABPA	chr6:166755671-166756366	A549	lung:	n/a	chr6:166756112-166756126 chr6:166756115-166756129 chr6:166756115-166756126
30	MYC	chr6:166755941-166756240	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr6:166755379-166756958	GM12891	blood:	n/a	n/a
32	ZNF384	chr6:166756043-166756430	K562	blood:	n/a	n/a
33	ELF1	chr6:166755686-166756535	SK-N-SH	brain:	n/a	n/a
34	HEY1	chr6:166755379-166756658	K562	blood:	n/a	chr6:166755859-166755874
35	TCF12	chr6:166755736-166756447	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr6:166755745-166756351	Hela-S3	cervix:	n/a	n/a
37	TCF12	chr6:166755603-166756455	ECC-1	luminal epithelium:	n/a	n/a
38	ELF1	chr6:166755709-166756461	HepG2	liver:	n/a	n/a
39	ZMIZ1	chr6:166755602-166756666	K562	blood:	n/a	n/a
40	POLR2A	chr6:166755446-166756921	GM19193	blood:	n/a	n/a
41	SIN3AK20	chr6:166755805-166756605	PANC-1	pancreas:	n/a	n/a
42	POLR2A	chr6:166755659-166756556	Hela-S3	cervix:	n/a	n/a
43	CREB1	chr6:166755673-166756859	HepG2	liver:	n/a	n/a
44	HEY1	chr6:166755845-166756645	HepG2	liver:	n/a	chr6:166755859-166755874
45	GTF2F1	chr6:166755952-166756303	Hela-S3	cervix:	n/a	n/a
46	TEAD4	chr6:166755836-166757023	K562	blood:	n/a	n/a
47	POLR2A	chr6:166755072-166758044	K562	blood:	n/a	n/a
48	POLR2A	chr6:166755808-166756517	H1-hESC	embryonic stem cell:	n/a	n/a
49	PAX5	chr6:166755701-166756771	GM12878	blood:	n/a	chr6:166756095-166756104
50	PML	chr6:166755716-166757050	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:166756177-166756227	HEK293	kidney:	embryo
2	chr6:166756177-166756227	IMR90	lung:	fetal
3	chr6:166756177-166756227	GM06990	blood:	n/a
4	chr6:166756177-166756227	HCT-116	colon:	n/a
5	chr6:166756177-166756227	MCF10A-Er-Src	breast:	n/a
6	chr6:166756177-166756227	HIPEpiC	eye:	n/a
7	chr6:166756177-166756227	SAEC	small airway:	n/a
8	chr6:166756177-166756227	AG04450	lung:	fetal
9	chr6:166756177-166756227	NT2-D1	testis:	n/a
10	chr6:166756177-166756227	AG04449	skin:	fetal
11	chr6:166756177-166756227	HMEC	breast:	n/a
12	chr6:166756177-166756227	AG10803	skin:	n/a
13	chr6:166756177-166756227	GM12892	blood:	n/a
14	chr6:166756177-166756227	ProgFib	skin:	n/a
15	chr6:166756177-166756227	HRPEpiC	eye:	n/a
16	chr6:166756177-166756227	SK-N-SH	brain:	n/a
17	chr6:166756177-166756227	HCPEpiC	choroid plexus:	n/a
18	chr6:166756177-166756227	Jurkat	blood:	n/a
19	chr6:166756177-166756227	Caco-2	colon:	n/a
20	chr6:166756177-166756227	HNPCEpiC	eye:	n/a
21	chr6:166756177-166756227	HL-60	blood:	n/a
22	chr6:166756177-166756227	NHBE	bronchial:	n/a
23	chr6:166756177-166756227	H1-hESC	embryonic stem cell:	embryo
24	chr6:166756177-166756227	GM12891	blood:	n/a
25	chr6:166756177-166756227	PrEC	prostate:	n/a
26	chr6:166756177-166756227	NH-A	brain:	n/a
27	chr6:166756177-166756227	GM12878	blood:	n/a
28	chr6:166756177-166756227	HAEpiC	amniotic membrane:	n/a
29	chr6:166756177-166756227	SK-N-SH_RA	brain:	n/a
30	chr6:166756177-166756227	PFSK-1	brain:	n/a
31	chr6:166756177-166756227	HRE	kidney:	n/a
32	chr6:166756177-166756227	SK-N-MC	brain:	n/a
33	chr6:166756177-166756227	MCF-7	breast:	n/a
34	chr6:166756177-166756227	NB4	blood:	n/a
35	chr6:166756177-166756227	K562	blood:	n/a
36	chr6:166756177-166756227	AoSMC	blood vessel:	n/a
37	chr6:166756177-166756227	PANC-1	pancreas:	n/a
38	chr6:166756177-166756227	LNCaP	prostate:	n/a
39	chr6:166756177-166756227	Hepatocyte	liver:	n/a
40	chr6:166756177-166756227	ECC-1	luminal epithelium:	n/a
41	chr6:166756177-166756227	HPAEpiC	pulmonary alveolar:	n/a
42	chr6:166756177-166756227	HRCEpiC	kidney:	n/a
43	chr6:166756177-166756227	Hela-S3	cervix:	n/a
44	chr6:166756177-166756227	AG09309	skin:	n/a
45	chr6:166756177-166756227	HepG2	liver:	n/a
46	chr6:166756177-166756227	T-47D	breast:	n/a
47	chr6:166756177-166756227	U87	brain:	n/a
48	chr6:166756177-166756227	SKMC	muscle:	n/a
49	chr6:166756177-166756227	NHDF-neo	bronchial:	n/a
50	chr6:166756177-166756227	AG09319	gingival:	n/a

(count:9 , 50 per page) page: 1

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:

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

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

No data

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

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10455809	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10455976	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10455977	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10455978	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10946152	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10946158	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10946160	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10946161	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11551053	0.90[ASN][1000 genomes]
rs11752886	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11753652	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11755305	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12198613	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209616	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12214281	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12214812	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12662924	0.86[EUR][1000 genomes]
rs1599841	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2294335	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144886	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144887	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4144888	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4709111	0.82[CHB][hapmap]
rs4710042	0.82[CHB][hapmap]
rs55936781	0.84[EUR][1000 genomes]
rs59337176	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66461381	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68016351	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6932631	0.86[CEU][hapmap]
rs73030701	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73263155	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73788236	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7740965	0.81[AMR][1000 genomes]
rs7753161	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7767887	0.84[ASN][1000 genomes]
rs7771603	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9348121	0.83[CHB][hapmap]
rs941683	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2294334	LOC401284	cis	multi-tissue	Pritchard
rs2294334	LOC135043	cis	multi-tissue	Pritchard
rs2294334		cis	Lymphoblastoid	GTEx
rs2294334	SFT2D1	cis	multi-tissue	Pritchard
rs2294334	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	chr6:166754800-166756200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:166754800-166756400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:166754800-166756600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:166754800-166756600	Active TSS	Hela-S3	cervix
10	chr6:166754800-166757000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr6:166754800-166757000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:166754800-166757000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:166754800-166757000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:166754800-166757000	Active TSS	Colonic Mucosa	Colon
15	chr6:166754800-166757200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:166755000-166756200	Active TSS	Primary T cells fromperipheralblood	blood
17	chr6:166755000-166756200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:166755000-166756200	Active TSS	Fetal Muscle Trunk	muscle
19	chr6:166755000-166756400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:166755000-166756600	Active TSS	Aorta	Aorta
21	chr6:166755000-166756600	Active TSS	Brain Substantia Nigra	brain
22	chr6:166755000-166756800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:166755000-166756800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr6:166755000-166756800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:166755000-166756800	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr6:166755000-166756800	Active TSS	Lung	lung
27	chr6:166755000-166756800	Active TSS	Ovary	ovary
28	chr6:166755000-166756800	Active TSS	Rectal Smooth Muscle	rectum
29	chr6:166755000-166756800	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr6:166755000-166756800	Active TSS	NHDF-Ad	bronchial
31	chr6:166755000-166757000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr6:166755000-166757000	Active TSS	H1 Cell Line	embryonic stem cell
33	chr6:166755000-166757000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:166755000-166757000	Active TSS	Left Ventricle	heart
35	chr6:166755000-166757000	Active TSS	Psoas Muscle	Psoas
36	chr6:166755000-166757200	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr6:166755000-166757200	Active TSS	A549	lung
38	chr6:166755000-166757200	Active TSS	NHLF	lung
39	chr6:166755200-166756200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:166755200-166756400	Active TSS	Primary B cells from peripheral blood	blood
41	chr6:166755200-166756400	Active TSS	Primary T cells from cord blood	blood
42	chr6:166755200-166756400	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr6:166755200-166756400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr6:166755200-166756400	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr6:166755200-166756400	Active TSS	Brain Hippocampus Middle	brain
46	chr6:166755200-166756400	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr6:166755200-166756600	Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr6:166755200-166756600	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr6:166755200-166756600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:166755200-166756600	Active TSS	Primary T helper naive cells from peripheral blood	blood

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