Variant report

Variant	rs2704587
Chromosome Location	chr4:89850005-89850006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-6	chr4:89849963-89850439	refGeneNc_1707_NR_002806

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10008568	0.84[ASN][1000 genomes]
rs1246629	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246631	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246632	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1246634	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1246642	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13149750	0.84[ASN][1000 genomes]
rs1379932	0.93[EUR][1000 genomes]
rs1379933	0.93[EUR][1000 genomes]
rs1458551	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1458562	0.83[ASN][1000 genomes]
rs1563689	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1812329	0.81[ASN][1000 genomes]
rs2045517	0.81[ASN][1000 genomes]
rs2125409	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2446300	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2446301	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2446303	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2446304	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2464520	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2464522	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464523	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464528	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609255	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2609258	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609259	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609260	0.84[ASN][1000 genomes]
rs2609261	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609262	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2609264	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609265	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2609279	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609280	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609282	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2704570	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2704581	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704582	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704583	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2704604	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869952	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4693978	0.84[ASN][1000 genomes]
rs6813090	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6815970	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6824218	0.81[ASN][1000 genomes]
rs7673818	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7674369	0.81[ASN][1000 genomes]
rs7682317	0.81[ASN][1000 genomes]
rs9997652	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[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:29 , 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	chr4:89838800-89852000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:89840800-89862800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:89843800-89851800	Weak transcription	Pancreas	Pancrea
6	chr4:89845400-89859600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr4:89845400-89866400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr4:89845600-89857600	Weak transcription	Gastric	stomach
9	chr4:89847000-89853600	Weak transcription	Right Ventricle	heart
10	chr4:89847200-89851800	Weak transcription	Aorta	Aorta
11	chr4:89847200-89854400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:89847200-89858800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:89847400-89851000	Weak transcription	Fetal Intestine Small	intestine
14	chr4:89847400-89851600	Weak transcription	Placenta	Placenta
15	chr4:89847400-89851800	Weak transcription	Fetal Stomach	stomach
16	chr4:89847400-89851800	Weak transcription	Ovary	ovary
17	chr4:89847400-89858200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:89847600-89850200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:89847800-89855400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr4:89848000-89851000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:89848400-89861000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:89848600-89851000	Weak transcription	Fetal Lung	lung
23	chr4:89848800-89850400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:89849000-89852800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr4:89849400-89850600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr4:89849400-89851600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:89849600-89852000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr4:89849800-89850400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:89849800-89851400	Weak transcription	Duodenum Mucosa	Duodenum

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