Variant report

Variant	rs10433881
Chromosome Location	chr4:90040847-90040848
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-3	chr4:90040435-90041022	ENSG00000270720.1

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10001420	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10028121	1.00[JPT][hapmap]
rs10033476	1.00[CHB][hapmap]
rs11734924	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12645173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12647095	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12649875	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13105546	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133608	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138927	0.96[ASN][1000 genomes]
rs1355836	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1355837	0.89[ASN][1000 genomes]
rs1398937	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1398938	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1398939	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1398941	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1398943	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513811	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513812	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1513823	0.89[ASN][1000 genomes]
rs1533288	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1533289	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1533294	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1708659	0.89[ASN][1000 genomes]
rs1708671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1708672	0.85[ASN][1000 genomes]
rs1708673	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1708683	0.89[ASN][1000 genomes]
rs1795730	0.81[ASN][1000 genomes]
rs1795735	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1795737	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1795740	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1828735	0.89[ASN][1000 genomes]
rs1996139	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2056013	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2102650	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464511	0.81[ASN][1000 genomes]
rs2609266	0.85[CEU][hapmap]
rs2670618	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2670619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2670620	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2670627	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2670628	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2704580	0.85[ASN][1000 genomes]
rs2704585	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2704592	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28559811	0.81[ASN][1000 genomes]
rs2869989	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28718401	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28869547	0.81[ASN][1000 genomes]
rs2904264	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4325981	0.96[ASN][1000 genomes]
rs4693987	0.96[ASN][1000 genomes]
rs6532100	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6532113	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823241	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826482	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6834297	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6843986	0.86[ASN][1000 genomes]
rs6845264	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6846010	0.92[ASN][1000 genomes]
rs7657630	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180333	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9307063	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs938265	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs938267	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999793	0.81[ASN][1000 genomes]
rs9999873	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	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
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:90033600-90045600	Weak transcription	Esophagus	oesophagus
5	chr4:90033600-90045600	Weak transcription	Pancreas	Pancrea
6	chr4:90033600-90049200	Weak transcription	Gastric	stomach
7	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
8	chr4:90033800-90042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr4:90034000-90041600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:90034000-90042400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:90034000-90044000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:90034200-90041000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:90034400-90043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
16	chr4:90034600-90041600	Weak transcription	Fetal Intestine Large	intestine
17	chr4:90034600-90042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:90035000-90043600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:90035200-90042600	Weak transcription	Fetal Intestine Small	intestine
21	chr4:90035200-90042600	Weak transcription	K562	blood
22	chr4:90035400-90044600	Weak transcription	Fetal Muscle Leg	muscle
23	chr4:90035600-90041000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:90035600-90041000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:90035600-90041800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:90035600-90043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:90035600-90044000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:90036200-90041000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr4:90036600-90044800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:90037000-90046200	Weak transcription	Primary T cells from cord blood	blood
31	chr4:90039200-90041200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:90039200-90042800	Weak transcription	HepG2	liver
33	chr4:90039200-90044600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:90039800-90043400	Weak transcription	Placenta	Placenta
35	chr4:90039800-90043800	Weak transcription	Liver	Liver
36	chr4:90040400-90041000	Enhancers	HMEC	breast
37	chr4:90040400-90041200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:90040400-90041200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr4:90040400-90041600	Enhancers	NH-A	brain
40	chr4:90040600-90041000	Weak transcription	NHEK	skin
41	chr4:90040600-90041400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:90040600-90041400	Enhancers	NHLF	lung
43	chr4:90040600-90042800	Enhancers	A549	lung
44	chr4:90040800-90041200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:90040800-90041400	Enhancers	NHDF-Ad	bronchial
46	chr4:90040800-90041400	Enhancers	Osteobl	bone
47	chr4:90040800-90041600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:90040800-90041600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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