Variant report

Variant	rs1806138
Chromosome Location	chr5:9157454-9157455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:9150640..9153251-chr5:9156234..9158472,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAS2R1-21	chr5:9157257-9157593	NONHSAT100329

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17238371	0.85[CEU][hapmap]
rs17239547	1.00[CEU][hapmap];0.85[MEX][hapmap]
rs1806144	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1806147	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723025	0.91[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs886508	1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs886510	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv880323	chr5:9100211-9157454	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	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
13	nsv1020815	chr5:9135207-9425649	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv498044	chr5:9143754-9402870	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv530183	chr5:9146506-9413373	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1806138	CTNND2	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9136800-9176400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:9136800-9189000	Weak transcription	Pancreas	Pancrea
3	chr5:9143600-9161000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:9145000-9158000	Weak transcription	Esophagus	oesophagus
5	chr5:9145200-9160800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:9145400-9163200	Weak transcription	Fetal Kidney	kidney
7	chr5:9145600-9235400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:9151000-9169000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:9151200-9168800	Weak transcription	NH-A	brain
10	chr5:9151600-9157800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:9152400-9171800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:9152600-9157600	Weak transcription	Right Ventricle	heart
13	chr5:9153600-9157800	Weak transcription	Fetal Heart	heart
14	chr5:9153800-9183400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:9154000-9226200	Weak transcription	Fetal Intestine Large	intestine
16	chr5:9154800-9160200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:9154800-9170200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:9154800-9173400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:9154800-9176200	Weak transcription	Fetal Intestine Small	intestine
20	chr5:9154800-9176400	Weak transcription	Aorta	Aorta
21	chr5:9155000-9161200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:9155000-9174200	Weak transcription	Liver	Liver
23	chr5:9155200-9158000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:9155400-9158200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr5:9156200-9158400	Enhancers	NHDF-Ad	bronchial
26	chr5:9156400-9157800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:9156400-9157800	Enhancers	Spleen	Spleen
28	chr5:9156400-9158000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:9156600-9157600	Enhancers	Fetal Muscle Trunk	muscle
30	chr5:9156600-9157800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:9156800-9166600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:9156800-9171400	Weak transcription	Fetal Stomach	stomach
33	chr5:9157000-9157800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr5:9157200-9158000	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:9157200-9164600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:9157400-9157600	Enhancers	Dnd41	blood
37	chr5:9157400-9167000	Weak transcription	Fetal Muscle Leg	muscle

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