Variant report

Variant	rs9829727
Chromosome Location	chr3:48723831-48723832
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:56)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:56 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:48722664-48724339	A549	lung:	n/a	chr3:48723416-48723432
2	POLR2A	chr3:48722946-48724229	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr3:48722857-48723936	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr3:48723760-48723910	HRPEpiC	eye:	n/a	n/a
5	MAZ	chr3:48722902-48723918	GM12878	blood:	n/a	chr3:48723332-48723341
6	ZBTB7A	chr3:48722643-48724035	ECC-1	luminal epithelium:	n/a	chr3:48723055-48723062
7	POLR2A	chr3:48722838-48723982	K562	blood:	n/a	n/a
8	RAD21	chr3:48722737-48724385	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr3:48722814-48723833	H1-hESC	embryonic stem cell:	n/a	chr3:48723416-48723432
10	POLR2A	chr3:48722839-48724162	HCT-116	colon:	n/a	n/a
11	POLR2A	chr3:48722878-48723844	GM19193	blood:	n/a	n/a
12	MAZ	chr3:48722833-48723973	IMR90	lung:	n/a	chr3:48723332-48723341
13	POLR2A	chr3:48722959-48723848	GM18951	blood:	n/a	n/a
14	POLR2A	chr3:48722881-48724298	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr3:48723741-48724827	PFSK-1	brain:	n/a	n/a
16	STAT5A	chr3:48722677-48723868	GM12878	blood:	n/a	n/a
17	CTCF	chr3:48723760-48723910	HVMF	connective:	n/a	n/a
18	MAZ	chr3:48722879-48724019	K562	blood:	n/a	chr3:48723332-48723341
19	POLR2A	chr3:48723763-48724159	GM12878	blood:	n/a	n/a
20	POLR2A	chr3:48722751-48724540	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr3:48722946-48725300	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr3:48723418-48727664	A549	lung:	n/a	n/a
23	POLR2A	chr3:48722978-48724153	HUVEC	blood vessel:	n/a	n/a
24	HA-E2F1	chr3:48722750-48723833	MCF-7	breast:	n/a	chr3:48723046-48723058
25	POLR2A	chr3:48723152-48724092	SK-N-SH	brain:	n/a	n/a
26	CTCF	chr3:48722683-48724561	SK-N-SH	brain:	n/a	chr3:48723416-48723432
27	POLR2A	chr3:48723802-48724393	HCT-116	colon:	n/a	n/a
28	POLR2A	chr3:48723790-48724156	GM12892	blood:	n/a	n/a
29	POLR2A	chr3:48722874-48727317	GM12892	blood:	n/a	n/a
30	SIN3A	chr3:48722776-48723866	H1-hESC	embryonic stem cell:	n/a	chr3:48722793-48722807
31	POLR2A	chr3:48723537-48724216	U87	brain:	n/a	n/a
32	POLR2A	chr3:48722860-48725381	SK-N-MC	brain:	n/a	n/a
33	PML	chr3:48722861-48723935	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:48722970-48724851	MCF-7	breast:	n/a	n/a
35	ZBTB7A	chr3:48723249-48723840	K562	blood:	n/a	n/a
36	POLR2A	chr3:48722923-48724053	GM18505	blood:	n/a	n/a
37	POLR2A	chr3:48722064-48725822	HepG2	liver:	n/a	n/a
38	POLR2A	chr3:48723014-48725451	SK-N-SH	brain:	n/a	n/a
39	POLR2A	chr3:48722899-48724423	ECC-1	luminal epithelium:	n/a	n/a
40	RUNX3	chr3:48722925-48723837	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:48722960-48723876	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr3:48722962-48723837	K562	blood:	n/a	n/a
43	ELF1	chr3:48722714-48723902	GM12878	blood:	n/a	chr3:48723039-48723051
44	CTCF	chr3:48722768-48723846	GM12891	blood:	n/a	chr3:48723416-48723432
45	POLR2A	chr3:48723060-48725786	GM12891	blood:	n/a	n/a
46	CTCF	chr3:48723780-48723930	HFF	foreskin:	n/a	n/a
47	CTCF	chr3:48723800-48723950	SK-N-SH_RA	brain:	n/a	n/a
48	MAX	chr3:48722707-48723967	HepG2	liver:	n/a	chr3:48723332-48723341
49	POLR2A	chr3:48722902-48724038	ECC-1	luminal epithelium:	n/a	n/a
50	CTCF	chr3:48723820-48723970	GM12864	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48646668..48648790-chr3:48722957..48725638,2	K562	blood:
2	chr3:48722838..48724823-chr3:48955919..48958463,2	K562	blood:
3	chr3:48700292..48701937-chr3:48721950..48724599,2	K562	blood:
4	chr3:48717071..48719987-chr3:48721738..48723845,3	MCF-7	breast:
5	chr3:48721678..48726571-chr3:48727447..48730865,5	K562	blood:
6	chr3:48699573..48703813-chr3:48719476..48724654,10	MCF-7	breast:
7	chr3:48699299..48703873-chr3:48715927..48726939,20	MCF-7	breast:
8	chr3:48596333..48598381-chr3:48723382..48725322,2	K562	blood:
9	chr3:48721882..48723836-chr3:48753260..48755276,2	K562	blood:
10	chr3:48720678..48725638-chr3:48726169..48732697,10	MCF-7	breast:
11	chr3:48671184..48673366-chr3:48722826..48724747,2	K562	blood:
12	chr3:48713537..48717616-chr3:48720627..48724588,5	MCF-7	breast:
13	chr3:48700180..48704062-chr3:48721751..48723924,3	K562	blood:

No data

Variant related genes	Relation type
NCKIPSD	TF binding region
ENSG00000221883	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000010256	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000068745	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13324192	0.86[AFR][1000 genomes]
rs28607362	0.87[AFR][1000 genomes]
rs9848493	0.87[AFR][1000 genomes]
rs9872722	0.87[AFR][1000 genomes]
rs9878262	0.86[AFR][1000 genomes]
rs9882667	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv590248	chr3:48716993-48727636	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48718800-48725600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:48720600-48724400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr3:48721200-48724000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:48721600-48724000	Active TSS	Rectal Smooth Muscle	rectum
5	chr3:48721600-48724200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:48721800-48724000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:48721800-48724000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr3:48722000-48724000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr3:48722200-48724000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr3:48722400-48724000	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr3:48722400-48724000	Active TSS	A549	lung
12	chr3:48722600-48724000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr3:48722600-48724000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:48722600-48724000	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr3:48722600-48724000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:48722600-48724000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:48722600-48724000	Active TSS	Primary T cells from cord blood	blood
18	chr3:48722600-48724000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:48722600-48724000	Active TSS	Fetal Brain Female	brain
20	chr3:48722600-48724000	Active TSS	Osteobl	bone
21	chr3:48722600-48724200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:48722600-48724200	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr3:48722800-48724000	Flanking Active TSS	Colonic Mucosa	Colon
24	chr3:48723000-48724000	Active TSS	Thymus	Thymus
25	chr3:48723400-48724000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr3:48723400-48724000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr3:48723400-48724000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:48723400-48724000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:48723400-48724000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:48723400-48724000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr3:48723400-48724000	Flanking Active TSS	Fetal Muscle Trunk	muscle
32	chr3:48723400-48724000	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr3:48723400-48724000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr3:48723400-48724000	Flanking Active TSS	Dnd41	blood
35	chr3:48723400-48724000	Flanking Active TSS	NHEK	skin
36	chr3:48723400-48724200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:48723400-48724200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:48723600-48724000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:48723600-48724000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:48723600-48724000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr3:48723600-48724000	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr3:48723600-48724000	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr3:48723600-48724000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr3:48723600-48724000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:48723600-48724000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:48723600-48724000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:48723600-48724000	Flanking Active TSS	Liver	Liver
48	chr3:48723600-48724000	Enhancers	Fetal Brain Male	brain
49	chr3:48723600-48724000	Enhancers	Fetal Kidney	kidney
50	chr3:48723600-48724000	Flanking Active TSS	Fetal Stomach	stomach

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