Variant report

Variant	rs34668230
Chromosome Location	chr3:46530458-46530459
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:306)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:306 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:46530194-46530530	GM10248	blood:	n/a	n/a
2	WRNIP1	chr3:46530265-46530588	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:46530366-46530569	H1-hESC	embryonic stem cell:	n/a	n/a
4	HDAC2	chr3:46530229-46530588	K562	blood:	n/a	n/a
5	IRF4	chr3:46530181-46530514	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:46530208-46530572	H1-hESC	embryonic stem cell:	n/a	n/a
7	BHLHE40	chr3:46530221-46530612	GM12878	blood:	n/a	n/a
8	CCNT2	chr3:46530236-46530802	K562	blood:	n/a	n/a
9	ZEB1	chr3:46530165-46530618	GM12878	blood:	n/a	n/a
10	JUND	chr3:46530147-46530611	K562	blood:	n/a	n/a
11	TCF12	chr3:46530235-46530620	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr3:46530205-46530509	GM20000	blood:	n/a	n/a
13	ELF1	chr3:46530188-46530784	K562	blood:	n/a	n/a
14	RAD21	chr3:46530129-46530661	ECC-1	luminal epithelium:	n/a	n/a
15	RCOR1	chr3:46530162-46530780	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr3:46530320-46530470	GM12869	blood:	n/a	n/a
17	MYC	chr3:46530156-46530625	K562	blood:	n/a	n/a
18	PAX5	chr3:46530212-46530689	GM12878	blood:	n/a	n/a
19	TEAD4	chr3:46530091-46530611	K562	blood:	n/a	n/a
20	EP300	chr3:46530245-46530712	HepG2	liver:	n/a	n/a
21	MAX	chr3:46530196-46530625	Hela-S3	cervix:	n/a	n/a
22	ATF2	chr3:46530151-46530620	H1-hESC	embryonic stem cell:	n/a	n/a
23	BACH1	chr3:46530281-46530548	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr3:46530319-46530495	HUVEC	blood vessel:	n/a	n/a
25	CUX1	chr3:46530231-46530555	GM12878	blood:	n/a	n/a
26	UBTF	chr3:46530215-46530689	K562	blood:	n/a	n/a
27	MAX	chr3:46530290-46530562	HepG2	liver:	n/a	n/a
28	CHD2	chr3:46530197-46530616	GM12878	blood:	n/a	n/a
29	CTCF	chr3:46530184-46530590	NHEK	skin:	n/a	n/a
30	CTCF	chr3:46530139-46530880	H1-hESC	embryonic stem cell:	n/a	n/a
31	TBP	chr3:46530196-46530549	K562	blood:	n/a	n/a
32	CTCF	chr3:46530181-46530533	GM10266	blood:	n/a	n/a
33	MYC	chr3:46530266-46530503	MCF10A-Er-Src	breast:	n/a	n/a
34	TBP	chr3:46530245-46530674	H1-hESC	embryonic stem cell:	n/a	n/a
35	RUNX3	chr3:46530159-46530646	GM12878	blood:	n/a	n/a
36	PAX5	chr3:46530211-46530589	GM12878	blood:	n/a	n/a
37	EP300	chr3:46530164-46530578	K562	blood:	n/a	n/a
38	MAX	chr3:46530164-46530801	ECC-1	luminal epithelium:	n/a	n/a
39	RAD21	chr3:46530064-46530663	A549	lung:	n/a	n/a
40	CTCF	chr3:46530173-46530547	LNCaP	prostate:	n/a	n/a
41	RAD21	chr3:46530153-46530617	K562	blood:	n/a	n/a
42	RAD21	chr3:46530192-46530540	GM12878	blood:	n/a	n/a
43	CTCF	chr3:46530194-46530547	Hela-S3	cervix:	n/a	n/a
44	TCF3	chr3:46530161-46530588	GM12878	blood:	n/a	n/a
45	ELF1	chr3:46530211-46530806	GM12878	blood:	n/a	n/a
46	FOS	chr3:46530272-46530464	MCF10A-Er-Src	breast:	n/a	n/a
47	BCLAF1	chr3:46530133-46530574	GM12878	blood:	n/a	n/a
48	RAD21	chr3:46530125-46530768	IMR90	lung:	n/a	n/a
49	ARID3A	chr3:46530187-46530494	K562	blood:	n/a	n/a
50	MAZ	chr3:46530157-46530637	K562	blood:	n/a	n/a

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46529857..46530830-chr3:46549274..46550154,2	K562	blood:
2	chr1:121484254..121485268-chr3:46529887..46530781,3	MCF-7	breast:
3	chr3:46530293..46531287-chr3:46600917..46601700,2	K562	blood:
4	chr3:46530235..46530934-chr3:46606775..46607619,4	K562	blood:
5	chr3:46441887..46442673-chr3:46529916..46530717,2	K562	blood:
6	chr3:46490983..46491780-chr3:46529871..46530687,2	MCF-7	breast:
7	chr3:46529979..46530787-chr3:46607787..46608328,2	K562	blood:
8	chr3:46529944..46530794-chr3:46705110..46706015,2	K562	blood:
9	chr3:46530210..46534355-chr3:46598500..46601064,4	K562	blood:
10	chr3:46491080..46491922-chr3:46530287..46530830,3	MCF-7	breast:
11	chr3:46529686..46530942-chr3:46599020..46600485,46	MCF-7	breast:
12	chr3:46530210..46534355-chr3:46597750..46601064,4	K562	blood:
13	chr3:46528809..46531447-chr3:46546904..46549677,2	K562	blood:
14	chr3:46529871..46530872-chr3:46670590..46672462,23	K562	blood:
15	chr2:171671918..171672781-chr3:46529676..46530675,2	MCF-7	breast:
16	chr3:46529825..46532011-chr3:46599266..46600570,56	K562	blood:
17	chr3:46529884..46530839-chr3:46671105..46672532,19	MCF-7	breast:
18	chr3:46529889..46530997-chr3:46599244..46600312,18	MCF-7	breast:
19	chr3:46529904..46530772-chr3:46603076..46604060,2	K562	blood:

No data

Variant related genes	Relation type
LTF	TF binding region
ENSG00000163827	Chromatin interaction
ENSG00000128683	Chromatin interaction
ENSG00000268324	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs13061783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13069424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13070959	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13076697	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13077283	0.88[ASN][1000 genomes]
rs13083022	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13093282	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099992	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13353428	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17078930	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17286758	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28539486	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28595844	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28617572	0.88[EUR][1000 genomes]
rs28670418	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28687398	0.86[EUR][1000 genomes]
rs34167705	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34227041	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34767161	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34850133	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35056755	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35082490	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35124447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35740565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35760835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35864396	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3934895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55689943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55702201	0.87[ASN][1000 genomes]
rs56106816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56288081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442003	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6442004	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66627456	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66702674	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66826527	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67091203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67222447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67228693	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67305272	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67647205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769817	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6770016	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770574	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6772291	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778305	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778415	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6778422	0.90[ASN][1000 genomes]
rs6783443	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6792420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67962987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801427	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804179	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68095529	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs71622507	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73067779	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73069915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73069952	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7624932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625793	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7626061	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7628435	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7648827	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9808967	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846026	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9865911	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9866206	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867359	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9871405	0.88[EUR][1000 genomes];0.90[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	nsv1014624	chr3:46463424-46549188	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1009892	chr3:46496775-46546918	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv536553	chr3:46496775-46546918	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46525000-46530600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:46527400-46530600	Weak transcription	HSMMtube	muscle
3	chr3:46529400-46534200	Enhancers	Dnd41	blood
4	chr3:46529800-46531200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr3:46530000-46531000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:46530000-46531600	Enhancers	Fetal Thymus	thymus
7	chr3:46530000-46531800	Enhancers	NH-A	brain
8	chr3:46530200-46530600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:46530200-46530600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:46530200-46530600	Enhancers	Rectal Smooth Muscle	rectum
11	chr3:46530200-46530600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
12	chr3:46530200-46530800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr3:46530200-46530800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:46530200-46530800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
15	chr3:46530200-46530800	Enhancers	Brain Anterior Caudate	brain
16	chr3:46530200-46530800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
17	chr3:46530200-46530800	Enhancers	Placenta	Placenta
18	chr3:46530200-46530800	Bivalent Enhancer	Fetal Stomach	stomach
19	chr3:46530200-46530800	Genic enhancers	Right Atrium	heart
20	chr3:46530200-46531000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:46530200-46531000	Enhancers	Fetal Intestine Large	intestine
22	chr3:46530200-46531000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr3:46530200-46531200	Enhancers	Primary B cells from peripheral blood	blood
24	chr3:46530200-46531200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:46530200-46531200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr3:46530200-46531800	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:46530200-46533800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:46530400-46530600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr3:46530400-46530600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:46530400-46530600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr3:46530400-46530600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:46530400-46530600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:46530400-46530600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:46530400-46530600	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr3:46530400-46530600	Bivalent Enhancer	Brain Germinal Matrix	brain
36	chr3:46530400-46530600	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr3:46530400-46530600	Enhancers	Ovary	ovary
38	chr3:46530400-46530600	Active TSS	A549	lung
39	chr3:46530400-46530600	Enhancers	GM12878-XiMat	blood
40	chr3:46530400-46530800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr3:46530400-46530800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:46530400-46530800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr3:46530400-46530800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr3:46530400-46530800	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr3:46530400-46530800	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr3:46530400-46530800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr3:46530400-46530800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr3:46530400-46530800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr3:46530400-46530800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr3:46530400-46530800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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