Variant report

Variant	rs7669140
Chromosome Location	chr4:90041559-90041560
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIGD2-4	chr4:90041199-90042022	NONHSAT097383

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10025332	0.85[ASN][1000 genomes]
rs10516826	0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10516828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12507349	0.91[ASN][1000 genomes]
rs1343921	0.88[JPT][hapmap]
rs1398945	0.91[ASN][1000 genomes]
rs1513820	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17015025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17768752	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17769356	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17770293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819929	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17820320	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17821105	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1921680	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2175821	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869974	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3822085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5026462	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55806245	0.86[ASN][1000 genomes]
rs55885459	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55987745	0.84[ASN][1000 genomes]
rs55996516	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56038841	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56111951	0.91[ASN][1000 genomes]
rs56147277	0.86[ASN][1000 genomes]
rs56165603	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56344658	0.91[ASN][1000 genomes]
rs56355329	0.91[ASN][1000 genomes]
rs56672432	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56719325	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59188553	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59283403	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59586695	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60213126	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60591238	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60751124	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61082288	0.86[ASN][1000 genomes]
rs62306393	1.00[ASN][1000 genomes]
rs6822256	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6825767	0.85[ASN][1000 genomes]
rs6825804	0.85[ASN][1000 genomes]
rs6826703	0.84[ASN][1000 genomes]
rs6832298	0.86[ASN][1000 genomes]
rs72665867	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72665868	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72665882	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72665892	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72665898	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72665902	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72668111	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72668112	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72668120	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72668125	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668127	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668130	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668134	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72668135	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668138	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72668144	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668152	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668154	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668156	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668157	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668165	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668167	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668171	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72668179	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72668183	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72668187	0.91[ASN][1000 genomes]
rs72668189	0.89[ASN][1000 genomes]
rs72668192	0.86[ASN][1000 genomes]
rs72668193	0.86[ASN][1000 genomes]
rs72668195	0.85[ASN][1000 genomes]
rs72668196	0.85[ASN][1000 genomes]
rs72670003	0.85[ASN][1000 genomes]
rs756227	0.85[ASN][1000 genomes]
rs7660709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.99[ASN][1000 genomes]
rs7689498	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9993181	0.89[JPT][hapmap]

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:40 , 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	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:90034400-90043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
15	chr4:90034600-90041600	Weak transcription	Fetal Intestine Large	intestine
16	chr4:90034600-90042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:90035000-90043600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:90035200-90042600	Weak transcription	Fetal Intestine Small	intestine
20	chr4:90035200-90042600	Weak transcription	K562	blood
21	chr4:90035400-90044600	Weak transcription	Fetal Muscle Leg	muscle
22	chr4:90035600-90041800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:90035600-90043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:90035600-90044000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:90036600-90044800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:90037000-90046200	Weak transcription	Primary T cells from cord blood	blood
27	chr4:90039200-90042800	Weak transcription	HepG2	liver
28	chr4:90039200-90044600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:90039800-90043400	Weak transcription	Placenta	Placenta
30	chr4:90039800-90043800	Weak transcription	Liver	Liver
31	chr4:90040400-90041600	Enhancers	NH-A	brain
32	chr4:90040600-90042800	Enhancers	A549	lung
33	chr4:90040800-90041600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:90040800-90041600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:90041000-90041600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:90041000-90043200	Weak transcription	HMEC	breast
37	chr4:90041200-90041600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:90041200-90042600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:90041200-90043200	Weak transcription	NHEK	skin
40	chr4:90041400-90043800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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