Variant report

Variant	rs60031743
Chromosome Location	chr9:98261032-98261033
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
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	CTCF	chr9:98261000-98261150	HCPEpiC	choroid plexus:	n/a	n/a
2	GATA3	chr9:98260927-98261374	MCF-7	breast:	n/a	n/a
3	CTCF	chr9:98260980-98261130	AG04449	skin:	n/a	n/a
4	CTCF	chr9:98261020-98261170	HCPEpiC	choroid plexus:	n/a	n/a
5	NR2F2	chr9:98260830-98261229	MCF-7	breast:	n/a	n/a
6	GATA3	chr9:98260950-98261251	MCF-7	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:98077549..98081770-chr9:98260761..98263260,3	MCF-7	breast:
2	chr9:98247307..98248885-chr9:98260285..98262282,2	MCF-7	breast:
3	chr9:98187019..98190552-chr9:98258756..98262395,5	MCF-7	breast:
4	chr9:98243031..98244911-chr9:98259333..98262016,2	K562	blood:
5	chr9:98255984..98258555-chr9:98260350..98263528,4	K562	blood:
6	chr9:98254931..98258273-chr9:98260384..98262387,3	MCF-7	breast:
7	chr9:98248561..98250430-chr9:98258742..98261519,2	MCF-7	breast:
8	chr9:98253775..98259048-chr9:98260307..98264013,8	K562	blood:

No data

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000237857	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000271314	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs28509458	0.98[AFR][1000 genomes]
rs28687112	0.98[AFR][1000 genomes]
rs28753971	0.86[AFR][1000 genomes]
rs60008840	0.93[AFR][1000 genomes]
rs61184807	0.93[AFR][1000 genomes]
rs73527759	0.84[AFR][1000 genomes]
rs73527766	0.87[AFR][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	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1051665	chr9:98234404-98264577	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
5	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
6	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
7	chr9:98249200-98263600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr9:98250400-98262800	Weak transcription	Stomach Mucosa	stomach
9	chr9:98253400-98262400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
11	chr9:98255600-98265000	Genic enhancers	Fetal Stomach	stomach
12	chr9:98256600-98261200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr9:98256600-98261800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:98257000-98261400	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr9:98257000-98262200	Weak transcription	HepG2	liver
16	chr9:98257000-98262800	Enhancers	Brain Substantia Nigra	brain
17	chr9:98257000-98264200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:98257000-98264200	Weak transcription	Gastric	stomach
19	chr9:98257400-98261200	Weak transcription	Colonic Mucosa	Colon
20	chr9:98257400-98261200	Weak transcription	Fetal Intestine Large	intestine
21	chr9:98257400-98262200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:98257400-98264400	Genic enhancers	Fetal Lung	lung
23	chr9:98257400-98266600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr9:98257400-98267000	Enhancers	Brain Hippocampus Middle	brain
25	chr9:98257600-98262200	Weak transcription	Fetal Heart	heart
26	chr9:98257600-98262200	Weak transcription	Pancreas	Pancrea
27	chr9:98257800-98261600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr9:98258000-98262000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr9:98258000-98264200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr9:98258000-98266400	Enhancers	Ovary	ovary
31	chr9:98258600-98262000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:98258600-98262200	Weak transcription	GM12878-XiMat	blood
33	chr9:98258600-98262600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:98258600-98266400	Weak transcription	Esophagus	oesophagus
35	chr9:98259200-98262400	Enhancers	Osteobl	bone
36	chr9:98259400-98261400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:98259400-98261400	Enhancers	Brain Cingulate Gyrus	brain
38	chr9:98259600-98261200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:98259600-98261400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr9:98259600-98261600	Enhancers	Left Ventricle	heart
41	chr9:98259600-98262400	Strong transcription	Fetal Intestine Small	intestine
42	chr9:98259600-98263000	Enhancers	Placenta	Placenta
43	chr9:98259600-98263000	Enhancers	Lung	lung
44	chr9:98259600-98263000	Enhancers	NHLF	lung
45	chr9:98259600-98266600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:98259800-98261400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:98259800-98263000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:98259800-98263000	Enhancers	Brain Anterior Caudate	brain
49	chr9:98260000-98261600	Enhancers	Colon Smooth Muscle	Colon
50	chr9:98260000-98261800	Enhancers	Brain Germinal Matrix	brain

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