Variant report

Variant	rs559471231
Chromosome Location	chr3:51703467-51703468
allele	C/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	CHD2	chr3:51703314-51703582	GM12878	blood:	n/a	n/a
2	CTCF	chr3:51703321-51703652	K562	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
3	GATA2	chr3:51703196-51703583	K562	blood:	n/a	chr3:51703347-51703363 chr3:51703341-51703358 chr3:51703352-51703359 chr3:51703352-51703359 chr3:51703345-51703366 chr3:51703323-51703336 chr3:51703352-51703359 chr3:51703350-51703359
4	CTCF	chr3:51703325-51703576	HepG2	liver:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
5	POU2F2	chr3:51703269-51703649	GM12878	blood:	n/a	n/a
6	MAZ	chr3:51703320-51703626	GM12878	blood:	n/a	n/a
7	CTCF	chr3:51703400-51703550	NHEK	skin:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
8	MAX	chr3:51703225-51703719	MCF-7	breast:	n/a	chr3:51703379-51703389
9	RAD21	chr3:51703226-51703678	IMR90	lung:	n/a	chr3:51703461-51703475 chr3:51703457-51703476 chr3:51703460-51703473 chr3:51703461-51703471
10	CTCF	chr3:51703337-51703624	H1-hESC	embryonic stem cell:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
11	CTCF	chr3:51703345-51703599	HepG2	liver:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
12	CTCF	chr3:51703319-51703644	MCF-7	breast:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
13	CTCF	chr3:51703306-51703648	GM12892	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
14	CTCF	chr3:51703192-51703674	HepG2	liver:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
15	CTCF	chr3:51703400-51703550	GM12872	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
16	CTCF	chr3:51703380-51703530	HEK293	kidney:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
17	IRF4	chr3:51703271-51703652	GM12878	blood:	n/a	n/a
18	CTCF	chr3:51703400-51703550	HBMEC	blood vessel:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
19	CTCF	chr3:51703380-51703530	SK-N-SH_RA	brain:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
20	CTCF	chr3:51703400-51703550	MCF-7	breast:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
21	MYC	chr3:51703280-51703519	Hela-S3	cervix:	n/a	chr3:51703379-51703389
22	CTCF	chr3:51703400-51703550	HL-60	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
23	MAX	chr3:51703124-51703633	MCF-7	breast:	n/a	chr3:51703379-51703389
24	RAD21	chr3:51703299-51703620	A549	lung:	n/a	chr3:51703461-51703475 chr3:51703457-51703476 chr3:51703460-51703473 chr3:51703461-51703471
25	CTCF	chr3:51703420-51703570	GM12867	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
26	CTCF	chr3:51703307-51703647	GM19240	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
27	CTCF	chr3:51703297-51703637	MCF-7	breast:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
28	YY1	chr3:51703270-51703623	GM12892	blood:	n/a	n/a
29	USF2	chr3:51703244-51703582	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr3:51703380-51703530	GM12868	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
31	FOXA1	chr3:51703304-51703561	T-47D	breast:	n/a	n/a
32	CTCF	chr3:51703380-51703530	GM12878	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
33	CTCF	chr3:51703317-51703638	Fibrobl	skin:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
34	MAZ	chr3:51703219-51703660	K562	blood:	n/a	n/a
35	CTCF	chr3:51703341-51703610	GM13977	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
36	CTCF	chr3:51703360-51703510	GM12864	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
37	MAX	chr3:51703143-51703650	SK-N-SH	brain:	n/a	chr3:51703379-51703389
38	ZNF143	chr3:51703271-51703674	GM12878	blood:	n/a	n/a
39	CTCF	chr3:51703400-51703550	Caco-2	colon:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
40	MYC	chr3:51703117-51703919	MCF10A-Er-Src	breast:	n/a	chr3:51703379-51703389
41	MAX	chr3:51703116-51703612	ECC-1	luminal epithelium:	n/a	chr3:51703379-51703389
42	CTCF	chr3:51703400-51703550	GM06990	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
43	CTCF	chr3:51703420-51703570	GM12866	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
44	RCOR1	chr3:51703312-51703733	GM12878	blood:	n/a	n/a
45	CTCF	chr3:51703299-51703661	GM19238	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
46	CTCF	chr3:51703297-51703659	A549	lung:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
47	RAD21	chr3:51703189-51703727	HepG2	liver:	n/a	chr3:51703461-51703475 chr3:51703457-51703476 chr3:51703460-51703473 chr3:51703461-51703471
48	CTCF	chr3:51703380-51703530	K562	blood:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
49	CTCF	chr3:51703400-51703550	HMF	breast:	n/a	chr3:51703461-51703474 chr3:51703465-51703474 chr3:51703462-51703472 chr3:51703454-51703475 chr3:51703459-51703477
50	POLR2A	chr3:51703237-51704163	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51535785..51536669-chr3:51703108..51703917,3	MCF-7	breast:
2	chr3:51689639..51691996-chr3:51702378..51704180,2	K562	blood:
3	chr3:51692768..51695628-chr3:51701276..51703775,2	K562	blood:
4	chr3:51694128..51695719-chr3:51702275..51704283,2	K562	blood:
5	chr3:51532096..51536424-chr3:51702408..51707498,7	K562	blood:
6	chr3:51702918..51706936-chr3:51707889..51711767,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IQCF6-2	chr3:51700250-51703672	NONHSAT089874

Variant related genes	Relation type
TEX264	TF binding region
ENSG00000164081	Chromatin interaction
ENSG00000145041	Chromatin interaction

Extended variants
information (count: 2 )
Associated
traits (count: 0)

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	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv965167	chr3:51702892-51707059	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51682200-51704400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:51690800-51704400	Weak transcription	HUVEC	blood vessel
3	chr3:51694200-51704800	Weak transcription	Psoas Muscle	Psoas
4	chr3:51694400-51704400	Weak transcription	Fetal Brain Male	brain
5	chr3:51694400-51704600	Weak transcription	NHDF-Ad	bronchial
6	chr3:51696200-51704400	Weak transcription	Fetal Kidney	kidney
7	chr3:51696600-51704200	Weak transcription	Small Intestine	intestine
8	chr3:51697200-51704600	Weak transcription	Brain Substantia Nigra	brain
9	chr3:51697400-51703600	Weak transcription	GM12878-XiMat	blood
10	chr3:51697400-51704400	Weak transcription	Brain Angular Gyrus	brain
11	chr3:51697400-51704400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:51697400-51704600	Weak transcription	Left Ventricle	heart
13	chr3:51697400-51704800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:51697400-51704800	Weak transcription	Aorta	Aorta
15	chr3:51697600-51704400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:51697800-51704400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:51697800-51704600	Weak transcription	HSMM	muscle
18	chr3:51698000-51703600	Weak transcription	Gastric	stomach
19	chr3:51698000-51704800	Weak transcription	Ovary	ovary
20	chr3:51698200-51704600	Weak transcription	NH-A	brain
21	chr3:51698400-51704400	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:51698400-51704600	Weak transcription	HSMMtube	muscle
23	chr3:51699400-51704400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:51699800-51704400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:51699800-51704400	Weak transcription	Brain Germinal Matrix	brain
26	chr3:51700000-51703800	Weak transcription	Lung	lung
27	chr3:51700000-51704400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:51700000-51704400	Weak transcription	Fetal Intestine Large	intestine
29	chr3:51700000-51704600	Weak transcription	Fetal Brain Female	brain
30	chr3:51700200-51703800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:51700600-51704600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:51701200-51704400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:51701200-51704600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:51701800-51704600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:51702000-51704600	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr3:51702400-51704600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr3:51702400-51704600	Weak transcription	Fetal Stomach	stomach
38	chr3:51702600-51703600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:51702600-51703600	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr3:51702600-51704400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:51702800-51703800	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr3:51702800-51703800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr3:51702800-51703800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:51702800-51704000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:51702800-51704000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:51702800-51704000	Enhancers	Hela-S3	cervix
47	chr3:51702800-51704400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:51702800-51704400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr3:51702800-51704400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr3:51702800-51704400	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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