Variant report

Variant	rs7045635
Chromosome Location	chr9:98533318-98533319
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	ATF2	chr9:98532916-98533400	H1-hESC	embryonic stem cell:	n/a	n/a
2	KAP1	chr9:98532794-98533425	HEK293	kidney:	n/a	n/a
3	SIN3A	chr9:98532898-98533388	H1-hESC	embryonic stem cell:	n/a	n/a
4	TCF7L2	chr9:98532900-98534041	HEK293	kidney:	n/a	n/a
5	KAP1	chr9:98532997-98534075	U2OS	brain:	n/a	n/a
6	MXI1	chr9:98533161-98533325	H1-hESC	embryonic stem cell:	n/a	n/a
7	GATA2	chr9:98533208-98533393	SH-SY5Y	brain:	n/a	chr9:98533338-98533345 chr9:98533331-98533352
8	TCF12	chr9:98533058-98533339	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98531848..98533634-chr9:98635544..98637181,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268926	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10817721	0.86[JPT][hapmap]
rs1344352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742753	0.84[AFR][1000 genomes]
rs4743306	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]
rs4743316	0.86[CHB][hapmap]
rs6478964	0.87[CHB][hapmap]
rs7029459	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7860168	0.81[AFR][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

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98527600-98533800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr9:98528000-98533600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:98529800-98533800	Weak transcription	Brain Anterior Caudate	brain
4	chr9:98529800-98534000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:98531600-98534000	Enhancers	Placenta	Placenta
6	chr9:98531800-98535600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:98532000-98533400	Enhancers	HepG2	liver
8	chr9:98532200-98534600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:98532200-98535400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:98532200-98535800	Enhancers	Fetal Intestine Small	intestine
11	chr9:98532400-98533800	Enhancers	Fetal Kidney	kidney
12	chr9:98532600-98533400	Enhancers	Fetal Muscle Leg	muscle
13	chr9:98532600-98533600	Enhancers	Stomach Smooth Muscle	stomach
14	chr9:98532600-98533800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
15	chr9:98532600-98534000	Enhancers	Ovary	ovary
16	chr9:98532600-98534400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
17	chr9:98532600-98535200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:98532600-98535400	Enhancers	Pancreas	Pancrea
19	chr9:98532800-98533400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr9:98532800-98533800	Enhancers	Fetal Lung	lung
21	chr9:98532800-98534200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:98532800-98534800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr9:98532800-98534800	Enhancers	Fetal Heart	heart
24	chr9:98532800-98535400	Enhancers	H1 Cell Line	embryonic stem cell
25	chr9:98533000-98533400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr9:98533000-98533400	Bivalent Enhancer	Fetal Stomach	stomach
27	chr9:98533000-98533800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:98533000-98533800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:98533000-98534000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr9:98533000-98534000	Enhancers	Adipose Nuclei	Adipose
31	chr9:98533000-98534200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr9:98533000-98534200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:98533000-98534200	Enhancers	Colonic Mucosa	Colon
34	chr9:98533000-98534200	Enhancers	Lung	lung
35	chr9:98533000-98534200	Enhancers	Stomach Mucosa	stomach
36	chr9:98533000-98534800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:98533000-98535000	Enhancers	Duodenum Mucosa	Duodenum
38	chr9:98533000-98535400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:98533000-98535400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr9:98533000-98536000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:98533200-98533600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr9:98533200-98533600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
43	chr9:98533200-98533800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr9:98533200-98533800	Enhancers	Colon Smooth Muscle	Colon
45	chr9:98533200-98534000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:98533200-98534400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
47	chr9:98533200-98535000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:98533200-98535600	Enhancers	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links