Variant report

Variant	rs2609281
Chromosome Location	chr4:89852075-89852076
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-6	chr4:89852029-89852191	refGeneNc_1707_NR_002806

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10001420	0.83[ASN][1000 genomes]
rs10019862	0.96[ASN][1000 genomes]
rs10028121	0.96[ASN][1000 genomes]
rs10033435	0.92[ASN][1000 genomes]
rs10033476	0.92[ASN][1000 genomes]
rs1246630	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246633	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1246635	0.81[EUR][1000 genomes]
rs1246637	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246638	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1246639	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1246641	1.00[ASN][1000 genomes]
rs1272570	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13106968	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13148439	0.96[ASN][1000 genomes]
rs1398938	0.83[ASN][1000 genomes]
rs1398939	0.83[ASN][1000 genomes]
rs1398941	0.83[ASN][1000 genomes]
rs1458552	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458553	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458555	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795730	0.83[ASN][1000 genomes]
rs1795737	0.83[ASN][1000 genomes]
rs1795740	0.83[ASN][1000 genomes]
rs1903004	0.96[ASN][1000 genomes]
rs1903009	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045516	1.00[ASN][1000 genomes]
rs2125410	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2446295	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446302	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2446309	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464511	0.83[ASN][1000 genomes]
rs2464521	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464526	0.96[ASN][1000 genomes]
rs2609254	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609263	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2609266	0.96[ASN][1000 genomes]
rs2609274	1.00[ASN][1000 genomes]
rs2609278	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609284	0.92[ASN][1000 genomes]
rs2670619	0.83[ASN][1000 genomes]
rs2670620	0.83[ASN][1000 genomes]
rs2704572	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2704588	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704591	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704593	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2704602	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704603	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2704606	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28559811	0.83[ASN][1000 genomes]
rs28624770	0.96[ASN][1000 genomes]
rs28658282	0.96[ASN][1000 genomes]
rs2869965	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2869968	1.00[ASN][1000 genomes]
rs28869547	0.83[ASN][1000 genomes]
rs4498109	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59698155	0.96[ASN][1000 genomes]
rs7673427	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7697878	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs922027	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs973680	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs987314	1.00[ASN][1000 genomes]
rs993358	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9999793	0.83[ASN][1000 genomes]
rs9999873	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1009354	chr4:89725914-89985155	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv998651	chr4:89800245-89933445	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv537175	chr4:89800245-89933445	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv879532	chr4:89811195-89917135	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv879533	chr4:89832532-89917135	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89820000-89859200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:89825600-89878400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr4:89840800-89862800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:89845400-89859600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr4:89845400-89866400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:89845600-89857600	Weak transcription	Gastric	stomach
7	chr4:89847000-89853600	Weak transcription	Right Ventricle	heart
8	chr4:89847200-89854400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr4:89847200-89858800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr4:89847400-89858200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:89847800-89855400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr4:89848400-89861000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:89849000-89852800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:89850200-89878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:89850400-89861200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:89850600-89852600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:89850600-89853800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:89851000-89852400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr4:89851000-89852600	ZNF genes & repeats	Fetal Intestine Small	intestine
20	chr4:89851400-89852400	Active TSS	Duodenum Mucosa	Duodenum
21	chr4:89851400-89859200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:89851400-89883600	Weak transcription	Fetal Intestine Large	intestine
23	chr4:89851600-89852400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:89851600-89852600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:89851600-89852600	ZNF genes & repeats	Fetal Muscle Leg	muscle
26	chr4:89851600-89852600	Genic enhancers	Placenta	Placenta
27	chr4:89851800-89852400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:89851800-89852400	ZNF genes & repeats	Aorta	Aorta
29	chr4:89851800-89852400	Strong transcription	Fetal Lung	lung
30	chr4:89851800-89852400	Strong transcription	Ovary	ovary
31	chr4:89851800-89852400	Strong transcription	Pancreas	Pancrea
32	chr4:89851800-89852600	Strong transcription	Fetal Stomach	stomach
33	chr4:89852000-89852600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
34	chr4:89852000-89855200	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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