Variant report

Variant	rs4744330
Chromosome Location	chr9:97028749-97028750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11789111	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11791327	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11791619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11792912	0.83[AMR][1000 genomes]
rs11793128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11795331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12003203	0.89[AFR][1000 genomes]
rs12343123	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1536690	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1878875	0.85[JPT][hapmap]
rs4602957	0.86[AFR][1000 genomes]
rs56849060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58759607	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs59962706	0.87[AFR][1000 genomes]
rs62578818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578821	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62578822	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs62578823	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6479545	0.82[CHB][hapmap]
rs7019137	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7025878	0.85[JPT][hapmap]
rs7034153	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7036474	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7037298	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7045712	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7046779	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs722353	0.82[JPT][hapmap]
rs7854893	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7859571	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7871267	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7874441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9299417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9632920	0.85[CHB][hapmap];0.82[JPT][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	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
2	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	195 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4744330	RP11-307E17.8	cis	Esophagus Muscularis	GTEx
rs4744330	FLJ14753	cis	multi-tissue	Pritchard
rs4744330	HIATL1	cis	lung	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97022200-97031400	Weak transcription	Left Ventricle	heart
2	chr9:97022200-97031600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:97022200-97031600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:97022200-97031600	Weak transcription	HSMMtube	muscle
5	chr9:97022200-97033400	Weak transcription	Fetal Stomach	stomach
6	chr9:97022200-97040800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:97022200-97041800	Weak transcription	Fetal Lung	lung
8	chr9:97022200-97042600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr9:97022200-97055200	Weak transcription	Aorta	Aorta
10	chr9:97022400-97031400	Weak transcription	NHEK	skin
11	chr9:97022400-97036200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:97022600-97028800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:97022600-97029200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:97022600-97040600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:97022600-97055200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:97022800-97029200	Weak transcription	HSMM	muscle
17	chr9:97022800-97031400	Weak transcription	Psoas Muscle	Psoas
18	chr9:97022800-97040800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr9:97022800-97040800	Weak transcription	Thymus	Thymus
20	chr9:97022800-97042400	Weak transcription	Brain Angular Gyrus	brain
21	chr9:97022800-97054600	Weak transcription	Pancreas	Pancrea
22	chr9:97023000-97029000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr9:97023000-97029200	Weak transcription	Spleen	Spleen
24	chr9:97023000-97029800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr9:97023000-97030000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:97023000-97031600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:97023000-97036400	Weak transcription	Primary T cells from cord blood	blood
28	chr9:97023000-97040600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr9:97023000-97040600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:97023000-97040600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:97023000-97040600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:97023000-97040600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr9:97023000-97040800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:97023000-97040800	Weak transcription	Lung	lung
35	chr9:97023000-97041000	Weak transcription	Adipose Nuclei	Adipose
36	chr9:97023000-97041000	Weak transcription	Ovary	ovary
37	chr9:97023000-97041800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:97023000-97041800	Weak transcription	Esophagus	oesophagus
39	chr9:97023000-97050000	Weak transcription	Right Ventricle	heart
40	chr9:97023000-97055400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:97023200-97029400	Weak transcription	Hela-S3	cervix
42	chr9:97023400-97042800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:97023600-97040800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:97024000-97041200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr9:97024200-97035000	Weak transcription	GM12878-XiMat	blood
46	chr9:97024400-97040400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr9:97025600-97029400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr9:97026200-97033600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:97026600-97028800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
50	chr9:97027000-97040600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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