Variant report

Variant	rs4743306
Chromosome Location	chr9:98534372-98534373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:98534256-98534577	HepG2	liver:	n/a	n/a
2	HEY1	chr9:98533771-98534599	HepG2	liver:	n/a	n/a
3	CEBPD	chr9:98534271-98534523	HepG2	liver:	n/a	n/a
4	POLR2A	chr9:98533803-98535405	HepG2	liver:	n/a	n/a
5	MAZ	chr9:98534350-98534571	HepG2	liver:	n/a	chr9:98534434-98534444
6	POLR2A	chr9:98533749-98535412	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:98534327-98534377	HAEpiC	amniotic membrane:	n/a
2	chr9:98534327-98534377	ovcar-3	ovarian:	n/a
3	chr9:98534327-98534377	MCF10A-Er-Src	breast:	n/a
4	chr9:98534327-98534377	Jurkat	blood:	n/a
5	chr9:98534327-98534377	AG10803	skin:	n/a
6	chr9:98534327-98534377	GM06990	blood:	n/a
7	chr9:98534327-98534377	BJ	skin:	n/a
8	chr9:98534327-98534377	HEEpiC	esophagus:	n/a
9	chr9:98534327-98534377	SK-N-SH_RA	brain:	n/a
10	chr9:98534327-98534377	NH-A	brain:	n/a
11	chr9:98534327-98534377	MCF-7	breast:	n/a
12	chr9:98534327-98534377	HepG2	liver:	n/a
13	chr9:98534327-98534377	U87	brain:	n/a
14	chr9:98534327-98534377	ECC-1	luminal epithelium:	n/a
15	chr9:98534327-98534377	IMR90	lung:	fetal
16	chr9:98534327-98534377	PFSK-1	brain:	n/a
17	chr9:98534327-98534377	HIPEpiC	eye:	n/a
18	chr9:98534327-98534377	HRPEpiC	eye:	n/a
19	chr9:98534327-98534377	NHBE	bronchial:	n/a
20	chr9:98534327-98534377	NT2-D1	testis:	n/a
21	chr9:98534327-98534377	Hela-S3	cervix:	n/a
22	chr9:98534327-98534377	GM19239	blood:	n/a
23	chr9:98534327-98534377	AG09319	gingival:	n/a
24	chr9:98534327-98534377	LNCaP	prostate:	n/a
25	chr9:98534327-98534377	H1-hESC	embryonic stem cell:	embryo
26	chr9:98534327-98534377	HMEC	breast:	n/a
27	chr9:98534327-98534377	CMK	blood:	n/a
28	chr9:98534327-98534377	HL-60	blood:	n/a
29	chr9:98534327-98534377	SAEC	small airway:	n/a
30	chr9:98534327-98534377	A549	lung:	n/a
31	chr9:98534327-98534377	Caco-2	colon:	n/a
32	chr9:98534327-98534377	Hepatocyte	liver:	n/a
33	chr9:98534327-98534377	K562	blood:	n/a
34	chr9:98534327-98534377	HRCEpiC	kidney:	n/a
35	chr9:98534327-98534377	PANC-1	pancreas:	n/a
36	chr9:98534327-98534377	HEK293	kidney:	embryo
37	chr9:98534327-98534377	HPAEpiC	pulmonary alveolar:	n/a
38	chr9:98534327-98534377	HCM	heart:	n/a
39	chr9:98534327-98534377	AoSMC	blood vessel:	n/a
40	chr9:98534327-98534377	AG04450	lung:	fetal
41	chr9:98534327-98534377	GM12891	blood:	n/a
42	chr9:98534327-98534377	HCF	heart:	n/a
43	chr9:98534327-98534377	GM12892	blood:	n/a
44	chr9:98534327-98534377	HRE	kidney:	n/a
45	chr9:98534327-98534377	SKMC	muscle:	n/a
46	chr9:98534327-98534377	SK-N-MC	brain:	n/a
47	chr9:98534327-98534377	NHDF-neo	bronchial:	n/a
48	chr9:98534327-98534377	HUVEC	blood vessel:	n/a
49	chr9:98534327-98534377	BE2_C	brain:	n/a
50	chr9:98534327-98534377	HNPCEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98534328..98536116-chr9:98636365..98638226,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268926	TF binding region
ENSG00000268926	CpG island
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10817721	0.87[JPT][hapmap]
rs12347549	0.84[CHD][hapmap];0.80[MEX][hapmap]
rs1344352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1836406	0.92[ASW][hapmap]
rs4743316	0.86[CHB][hapmap]
rs6478964	0.86[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6478965	0.82[AFR][1000 genomes]
rs7029459	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7045260	0.82[AFR][1000 genomes]
rs7045635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4743306	SLC35D2	cis	parietal	SCAN
rs4743306	FBP1	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98531800-98535600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:98532200-98534600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:98532200-98535400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:98532200-98535800	Enhancers	Fetal Intestine Small	intestine
5	chr9:98532600-98534400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
6	chr9:98532600-98535200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:98532600-98535400	Enhancers	Pancreas	Pancrea
8	chr9:98532800-98534800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr9:98532800-98534800	Enhancers	Fetal Heart	heart
10	chr9:98532800-98535400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr9:98533000-98534800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:98533000-98535000	Enhancers	Duodenum Mucosa	Duodenum
13	chr9:98533000-98535400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:98533000-98535400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr9:98533000-98536000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:98533200-98534400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
17	chr9:98533200-98535000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr9:98533200-98535600	Enhancers	Fetal Intestine Large	intestine
19	chr9:98533400-98534400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr9:98533400-98535600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr9:98533400-98535600	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr9:98533400-98535800	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr9:98533400-98536200	Enhancers	Fetal Stomach	stomach
24	chr9:98533600-98534400	Enhancers	NHLF	lung
25	chr9:98533600-98535200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr9:98533600-98535200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:98533600-98535400	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr9:98533800-98534400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:98533800-98534400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr9:98533800-98534400	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr9:98533800-98534400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:98533800-98534400	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr9:98533800-98534600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:98533800-98534600	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr9:98533800-98534600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
36	chr9:98533800-98534600	Active TSS	HepG2	liver
37	chr9:98533800-98534800	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr9:98533800-98534800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr9:98533800-98534800	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr9:98533800-98534800	Enhancers	HSMMtube	muscle
41	chr9:98533800-98535000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:98533800-98535000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr9:98533800-98535000	Weak transcription	Fetal Kidney	kidney
44	chr9:98533800-98535200	Bivalent Enhancer	Fetal Brain Male	brain
45	chr9:98533800-98535400	Enhancers	Brain Angular Gyrus	brain
46	chr9:98533800-98535800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:98533800-98535800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:98533800-98535800	Enhancers	HSMM	muscle
49	chr9:98533800-98536000	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr9:98534000-98534400	Enhancers	Liver	Liver

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