Variant report

Variant	rs3824487
Chromosome Location	chr9:98222651-98222652
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	GATA2	chr9:98220930-98223160	SH-SY5Y	brain:	n/a	chr9:98223037-98223047

Variant related genes	Relation type
PTCH1	TF binding region

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

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

rs_ID	r²[population]
rs16905572	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2066835	0.91[AFR][1000 genomes]
rs2236405	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274690	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277183	0.92[ASN][1000 genomes]
rs2277184	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28413575	0.94[ASN][1000 genomes]
rs28735184	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	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
5	nsv1053762	chr9:98208542-98232120	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1047465	chr9:98217524-98228225	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98202000-98224600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:98204800-98224400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:98206000-98224400	Weak transcription	HUVEC	blood vessel
4	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
5	chr9:98206600-98223000	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:98206600-98224000	Strong transcription	Adipose Nuclei	Adipose
7	chr9:98206600-98224600	Strong transcription	Aorta	Aorta
8	chr9:98206600-98225200	Strong transcription	Pancreas	Pancrea
9	chr9:98207000-98223000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr9:98207200-98223200	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr9:98207200-98224400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:98207400-98224200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:98207600-98224400	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr9:98208000-98224400	Weak transcription	HSMM	muscle
15	chr9:98208600-98224000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:98209600-98224000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:98209600-98224400	Weak transcription	NHDF-Ad	bronchial
18	chr9:98210400-98223800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:98211200-98224200	Strong transcription	Left Ventricle	heart
20	chr9:98211400-98224600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr9:98212000-98224600	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:98213200-98224600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:98213600-98224000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr9:98213600-98224400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:98214200-98224200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr9:98214200-98224400	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr9:98214200-98225400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:98214400-98224200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:98214400-98224200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:98214800-98223600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:98214800-98224000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:98215200-98224600	Weak transcription	Osteobl	bone
33	chr9:98215400-98224200	Strong transcription	Right Ventricle	heart
34	chr9:98215600-98224200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr9:98216800-98223200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr9:98216800-98224000	Weak transcription	Stomach Mucosa	stomach
37	chr9:98217600-98223400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr9:98217600-98224200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:98218000-98224000	Strong transcription	Liver	Liver
40	chr9:98218000-98224400	Strong transcription	HepG2	liver
41	chr9:98218200-98223800	Strong transcription	K562	blood
42	chr9:98218800-98224400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:98218800-98227400	Genic enhancers	Fetal Stomach	stomach
44	chr9:98219000-98224400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:98219000-98224400	Weak transcription	NHEK	skin
46	chr9:98219200-98223000	Weak transcription	A549	lung
47	chr9:98219400-98224200	Weak transcription	Small Intestine	intestine
48	chr9:98219400-98225400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr9:98219800-98223400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr9:98219800-98223600	Enhancers	Colon Smooth Muscle	Colon

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