Variant report

Variant	rs2869966
Chromosome Location	chr4:89869078-89869079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-6	chr4:89868009-89870277	refGeneNc_1707_NR_002806

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10008568	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1246642	0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs13149750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1458562	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1812329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1903003	0.82[CHD][hapmap];0.81[ASN][1000 genomes]
rs1964516	0.90[ASN][1000 genomes]
rs2013701	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs2045517	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2125409	0.86[ASN][1000 genomes]
rs2446300	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2446301	0.82[CHB][hapmap]
rs2464522	0.82[ASN][1000 genomes]
rs2464523	0.82[ASN][1000 genomes]
rs2464528	0.84[CHD][hapmap]
rs2609255	0.84[CHD][hapmap]
rs2609258	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2609259	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2609261	0.83[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs2609262	0.83[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs2609264	0.84[CHD][hapmap]
rs2609279	0.82[CHB][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2609280	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2704589	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs2869967	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2904259	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[ASN][1000 genomes]
rs3846287	0.82[ASN][1000 genomes]
rs4416442	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4505789	0.88[ASN][1000 genomes]
rs4693974	0.84[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs4693978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4693980	0.82[ASN][1000 genomes]
rs6824218	0.91[ASN][1000 genomes]
rs6837671	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6849143	0.80[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs6852928	0.80[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs7671167	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[ASN][1000 genomes]
rs7671261	0.82[ASN][1000 genomes]
rs7674369	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7682317	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7690839	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	esv1829430	chr4:89853598-89908308	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Chronic obstructive pulmonary disease	25241909	GWAS catalog

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:89825600-89878400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:89850200-89878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:89851400-89883600	Weak transcription	Fetal Intestine Large	intestine
4	chr4:89852400-89885000	Weak transcription	Fetal Lung	lung
5	chr4:89852600-89877800	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:89852600-89879200	Weak transcription	Fetal Stomach	stomach
7	chr4:89852600-89879400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr4:89856200-89869200	Weak transcription	Left Ventricle	heart
9	chr4:89856400-89872000	Weak transcription	Aorta	Aorta
10	chr4:89857800-89869600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:89857800-89872000	Weak transcription	Pancreas	Pancrea
12	chr4:89857800-89879400	Weak transcription	Lung	lung
13	chr4:89859600-89872000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:89859600-89877800	Weak transcription	Fetal Intestine Small	intestine
15	chr4:89861600-89873200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:89861600-89874600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:89863000-89874600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:89864400-89881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:89864800-89870400	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:89865400-89869200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:89865400-89870200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:89865400-89874600	Weak transcription	Primary T cells from cord blood	blood
23	chr4:89865600-89870800	Weak transcription	Ovary	ovary
24	chr4:89865600-89878400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr4:89865800-89870400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:89866600-89869400	Weak transcription	Fetal Kidney	kidney
27	chr4:89868000-89877200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:89868200-89875800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:89868400-89869200	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links