Variant report

Variant	rs56319302
Chromosome Location	chr9:94900555-94900556
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	CTCF	chr9:94900006-94901137	A549	lung:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
2	CTCF	chr9:94900480-94900630	GM12865	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
3	CTCF	chr9:94900480-94900630	GM12870	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
4	CTCF	chr9:94900450-94900701	Lung_OC	lung:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
5	CTCF	chr9:94900520-94900670	GM12870	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
6	YY1	chr9:94900386-94900687	H1-hESC	embryonic stem cell:	n/a	chr9:94900651-94900662
7	CTCF	chr9:94900371-94900796	MCF-7	breast:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
8	RAD21	chr9:94900394-94900790	MCF-7	breast:	n/a	chr9:94900560-94900579 chr9:94900561-94900570 chr9:94900565-94900577 chr9:94900561-94900575
9	HMGN3	chr9:94900436-94900597	K562	blood:	n/a	n/a
10	SMC3	chr9:94900393-94900772	Hela-S3	cervix:	n/a	chr9:94900561-94900575 chr9:94900561-94900568 chr9:94900565-94900575
11	CTCF	chr9:94900204-94900704	Pancreas_OC	pancreas:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
12	POLR2A	chr9:94900456-94901941	HepG2	liver:	n/a	n/a
13	CTCF	chr9:94900324-94900779	IMR90	lung:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
14	CTCF	chr9:94900480-94900630	HVMF	connective:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
15	MAX	chr9:94900437-94900614	NB4	blood:	n/a	chr9:94900481-94900490
16	YY1	chr9:94900474-94900626	K562	blood:	n/a	n/a
17	CTCF	chr9:94900480-94900630	HUVEC	blood vessel:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
18	CTCF	chr9:94900480-94900630	HL-60	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
19	CTCF	chr9:94900365-94900708	Kidney_OC	kidney:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
20	CTCF	chr9:94900480-94900630	HMEC	breast:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
21	CTCF	chr9:94900480-94900630	HCPEpiC	choroid plexus:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
22	POLR2A	chr9:94900453-94900641	IMR90	lung:	n/a	n/a
23	CTCF	chr9:94900500-94900650	SAEC	small airway:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
24	CTCF	chr9:94900480-94900630	K562	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
25	CTCF	chr9:94900480-94900630	GM12878	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
26	CTCF	chr9:94900480-94900630	BJ	skin:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
27	RAD21	chr9:94900383-94900758	GM12878	blood:	n/a	chr9:94900560-94900579 chr9:94900561-94900570 chr9:94900565-94900577 chr9:94900561-94900575
28	RAD21	chr9:94900229-94900982	SK-N-SH	brain:	n/a	chr9:94900560-94900579 chr9:94900561-94900570 chr9:94900565-94900577 chr9:94900561-94900575
29	CTCF	chr9:94900480-94900630	HA-sp	spinal cord:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
30	RAD21	chr9:94900392-94900774	GM12878	blood:	n/a	chr9:94900560-94900579 chr9:94900561-94900570 chr9:94900565-94900577 chr9:94900561-94900575
31	CTCF	chr9:94900480-94900630	NB4	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
32	RAD21	chr9:94900393-94900780	H1-hESC	embryonic stem cell:	n/a	chr9:94900560-94900579 chr9:94900561-94900570 chr9:94900565-94900577 chr9:94900561-94900575
33	CTCF	chr9:94900333-94900796	GM12878	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
34	CTCF	chr9:94900520-94900670	HCT-116	colon:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
35	CTCF	chr9:94900441-94900711	HUVEC	blood vessel:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
36	CTCF	chr9:94900414-94900728	Gliobla	brain:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
37	CTCF	chr9:94900460-94900634	SK-N-SH_RA	brain:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
38	MAX	chr9:94900433-94901112	HepG2	liver:	n/a	chr9:94900481-94900490
39	MAZ	chr9:94900385-94900673	GM12878	blood:	n/a	chr9:94900481-94900490
40	CTCF	chr9:94900500-94900650	SK-N-SH_RA	brain:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
41	CTCF	chr9:94900437-94900695	ProgFib	skin:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
42	CTCFL	chr9:94900491-94900636	K562	blood:	n/a	chr9:94900566-94900575
43	CTCF	chr9:94900239-94900740	NHEK	skin:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
44	ZNF143	chr9:94900385-94900767	GM12878	blood:	n/a	n/a
45	CTCF	chr9:94900480-94900630	HepG2	liver:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
46	CTCF	chr9:94900480-94900630	GM12872	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
47	CTCF	chr9:94900434-94900687	ECC-1	luminal epithelium:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
48	CTCF	chr9:94900500-94900650	Hela-S3	cervix:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
49	CTCF	chr9:94900244-94900716	GM10266	blood:	n/a	chr9:94900560-94900576 chr9:94900562-94900575 chr9:94900561-94900582 chr9:94900559-94900577 chr9:94900562-94900571 chr9:94900562-94900575 chr9:94900564-94900574
50	RAD21	chr9:94900287-94900846	H1-hESC	embryonic stem cell:	n/a	chr9:94900560-94900579 chr9:94900561-94900570 chr9:94900565-94900577 chr9:94900561-94900575

No.	Distal block	Cell Line	Cell type
1	chr9:94900132..94901096-chr9:95004214..95005474,7	MCF-7	breast:
2	chr9:94900325..94903739-chr9:94909399..94912070,4	MCF-7	breast:
3	chr9:94897533..94900717-chr9:94902765..94904749,3	MCF-7	breast:
4	chr9:94899508..94902437-chr9:95003923..95007845,5	MCF-7	breast:
5	chr9:94897363..94901349-chr9:95056061..95059787,4	K562	blood:
6	chr9:94898446..94901351-chr9:94903571..94905297,4	K562	blood:
7	chr9:94899081..94901349-chr9:95056061..95058658,2	K562	blood:
8	chr9:94898906..94903668-chr9:95086648..95090271,5	MCF-7	breast:
9	chr9:94900452..94902204-chr9:94914248..94916401,2	MCF-7	breast:
10	chr9:94899950..94900862-chr9:95004789..95005404,2	MCF-7	breast:
11	chr9:94899946..94902668-chr9:94908231..94910049,3	K562	blood:

Variant related genes	Relation type
LINC00475	TF binding region
ENSG00000225511	Chromatin interaction
ENSG00000196305	Chromatin interaction
ENSG00000198000	Chromatin interaction
ENSG00000188312	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10992240	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10992241	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10992244	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10992250	0.98[ASN][1000 genomes]
rs10992251	0.81[EUR][1000 genomes]
rs1970119	0.84[ASN][1000 genomes]
rs2398673	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35121804	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35814773	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3858094	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3927571	0.81[EUR][1000 genomes]
rs4391487	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55667598	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55801573	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62564361	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62564363	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62564364	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62568696	0.91[EUR][1000 genomes]
rs62568697	0.82[AFR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72748370	0.98[ASN][1000 genomes]
rs7465866	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94896400-94902400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:94896600-94902400	Weak transcription	Spleen	Spleen
3	chr9:94896600-94902800	Weak transcription	Gastric	stomach
4	chr9:94896800-94900800	Weak transcription	HSMMtube	muscle
5	chr9:94896800-94902600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr9:94896800-94902800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:94896800-94902800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr9:94896800-94902800	Weak transcription	Esophagus	oesophagus
9	chr9:94896800-94902800	Weak transcription	Right Atrium	heart
10	chr9:94896800-94902800	Weak transcription	A549	lung
11	chr9:94897000-94900800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:94897200-94901400	Weak transcription	NHLF	lung
13	chr9:94897200-94902400	Weak transcription	Ovary	ovary
14	chr9:94897200-94902800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr9:94897200-94902800	Weak transcription	HUVEC	blood vessel
16	chr9:94897400-94902400	Weak transcription	Osteobl	bone
17	chr9:94897400-94902800	Weak transcription	NHDF-Ad	bronchial
18	chr9:94897600-94902400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr9:94897600-94902800	Weak transcription	HMEC	breast
20	chr9:94899800-94901000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr9:94900000-94900600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
22	chr9:94900000-94900800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:94900000-94901800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:94900000-94903000	Flanking Active TSS	HepG2	liver
25	chr9:94900200-94900600	Enhancers	Primary B cells from peripheral blood	blood
26	chr9:94900200-94900600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr9:94900200-94900600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr9:94900200-94900600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr9:94900200-94900800	Enhancers	Brain Anterior Caudate	brain
30	chr9:94900200-94900800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr9:94900200-94900800	Enhancers	Fetal Muscle Leg	muscle
32	chr9:94900200-94900800	Enhancers	Dnd41	blood
33	chr9:94900200-94901000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr9:94900200-94901000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:94900200-94901400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr9:94900200-94901800	Enhancers	HSMM	muscle
37	chr9:94900200-94902600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:94900200-94902600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:94900200-94903200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr9:94900400-94900800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:94900400-94901000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:94900400-94902200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:94900400-94902400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:94900400-94902800	Weak transcription	Hela-S3	cervix
45	chr9:94900400-94902800	Weak transcription	K562	blood

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