Variant report

Variant	rs2993948
Chromosome Location	chr9:97176728-97176729
allele	A/G
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	GATA1	chr9:97175862-97176797	K562	blood:	n/a	n/a

Variant related genes	Relation type
HIATL1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10993182	0.83[ASN][1000 genomes]
rs10993186	0.89[ASN][1000 genomes]
rs10993188	0.87[ASN][1000 genomes]
rs11525963	0.87[ASN][1000 genomes]
rs12236578	0.81[ASN][1000 genomes]
rs16909983	0.82[ASN][1000 genomes]
rs1752784	0.82[CEU][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2104642	0.84[ASN][1000 genomes]
rs2486620	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2486632	0.87[CEU][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2769805	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2769813	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2769816	0.87[CEU][hapmap]
rs2809768	0.81[EUR][1000 genomes]
rs2809774	0.84[EUR][1000 genomes]
rs3118790	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4612412	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4744338	0.87[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4744345	0.87[CEU][hapmap];0.80[ASN][1000 genomes]
rs60964095	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs639276	0.87[CEU][hapmap];0.82[ASN][1000 genomes]
rs9409544	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9409546	0.87[CEU][hapmap];0.80[ASN][1000 genomes]
rs9409550	0.87[CEU][hapmap]

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	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1041195	chr9:97054795-97402378	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv982324	chr9:97139062-97200156	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2993948	HIATL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97153800-97182200	Weak transcription	NHEK	skin
2	chr9:97158000-97203200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr9:97160200-97182400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:97160200-97183400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr9:97160400-97203600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr9:97160800-97177000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:97164400-97185200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:97166400-97206400	Weak transcription	HSMMtube	muscle
9	chr9:97167800-97203600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr9:97169800-97207000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:97171800-97178800	Weak transcription	Fetal Intestine Small	intestine
12	chr9:97172000-97186000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr9:97172000-97203200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr9:97172000-97208400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr9:97172600-97204200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:97172800-97182400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:97173200-97184000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:97174200-97207000	Weak transcription	Lung	lung
19	chr9:97174400-97183800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:97175200-97178000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:97175600-97176800	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr9:97175600-97177000	Enhancers	K562	blood
23	chr9:97175600-97204200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:97175800-97202200	Weak transcription	Dnd41	blood
25	chr9:97176000-97177400	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr9:97176000-97183600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:97176000-97203800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:97176200-97178200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:97176200-97180200	Weak transcription	HSMM	muscle
30	chr9:97176200-97182200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr9:97176200-97182200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr9:97176200-97184600	Weak transcription	Primary T cells from cord blood	blood
33	chr9:97176200-97192200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:97176200-97194800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr9:97176200-97195000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:97176200-97201000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr9:97176200-97203200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr9:97176200-97203600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr9:97176200-97203600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:97176200-97207000	Weak transcription	Left Ventricle	heart
41	chr9:97176400-97177000	Weak transcription	Thymus	Thymus
42	chr9:97176400-97183600	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr9:97176400-97203200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr9:97176600-97177200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:97176600-97179200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:97176600-97183600	Weak transcription	Adipose Nuclei	Adipose
47	chr9:97176600-97203400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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