Variant report

Variant	rs17238371
Chromosome Location	chr5:9132002-9132003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAS2R1-22	chr5:9131997-9132274	NONHSAT100327

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1566894	0.91[EUR][1000 genomes]
rs17237055	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17237125	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17238053	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17238609	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17239547	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs17309469	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17316598	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1806138	0.85[CEU][hapmap]
rs1806147	0.85[CEU][hapmap]
rs1814177	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2892389	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41283163	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56196492	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56211009	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59536928	0.89[EUR][1000 genomes]
rs60224650	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61181903	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6897703	0.92[CEU][hapmap]
rs73045620	0.91[EUR][1000 genomes]
rs73740338	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73740340	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73740342	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73740343	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73740344	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73740345	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73740346	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73740358	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73741655	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73741659	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs886510	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv461944	chr5:8758041-9209831	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv597069	chr5:8758041-9209831	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1016937	chr5:8824417-9402871	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv537638	chr5:8824417-9402871	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv918004	chr5:8824417-9402871	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS 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	9 gene(s)	inside rSNPs	diseases
8	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
9	nsv830200	chr5:9081023-9269495	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv880683	chr5:9091164-9170323	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv881682	chr5:9100211-9151237	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv880323	chr5:9100211-9157454	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv597070	chr5:9100211-9280338	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv4707	chr5:9124819-9137589	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9105200-9145000	Weak transcription	Osteobl	bone
2	chr5:9108400-9135800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:9108800-9147600	Weak transcription	NHDF-Ad	bronchial
4	chr5:9116000-9144600	Weak transcription	Fetal Kidney	kidney
5	chr5:9117400-9135600	Weak transcription	Liver	Liver
6	chr5:9117600-9136400	Weak transcription	Fetal Heart	heart
7	chr5:9117600-9144600	Weak transcription	Fetal Lung	lung
8	chr5:9119200-9135000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr5:9119200-9153200	Weak transcription	Fetal Intestine Large	intestine
10	chr5:9119400-9134200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:9119400-9136000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:9119400-9136000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:9119400-9136400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:9119400-9144600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:9119400-9144600	Weak transcription	Fetal Intestine Small	intestine
16	chr5:9119400-9151800	Weak transcription	Left Ventricle	heart
17	chr5:9119400-9152000	Weak transcription	Right Ventricle	heart
18	chr5:9119400-9152000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:9119600-9144800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:9122800-9134400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:9123000-9132200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:9124400-9134600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:9124400-9138400	Weak transcription	Ovary	ovary
24	chr5:9124400-9144600	Weak transcription	Fetal Stomach	stomach
25	chr5:9124600-9135600	Weak transcription	Pancreas	Pancrea
26	chr5:9124600-9144600	Weak transcription	Aorta	Aorta
27	chr5:9126600-9135200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr5:9126800-9134000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr5:9127600-9134200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:9127600-9144000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:9128000-9134400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:9129200-9137400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:9130400-9137200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:9131000-9134000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:9131400-9134200	Weak transcription	Fetal Muscle Leg	muscle
36	chr5:9131400-9137000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:9131800-9132200	Enhancers	NHLF	lung
38	chr5:9131800-9132800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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