Variant report

Variant	rs13179890
Chromosome Location	chr5:9152182-9152183
allele	A/G
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-CCT5-29	chr5:9151947-9152392	NONHSAT100328

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12519438	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1806151	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1904454	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2256037	0.86[EUR][1000 genomes]
rs2256567	0.83[ASN][1000 genomes]
rs2256569	0.83[ASN][1000 genomes]
rs2526118	0.83[ASN][1000 genomes]
rs2619916	0.83[ASN][1000 genomes]
rs6862429	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs886509	0.86[EUR][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

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9119200-9153200	Weak transcription	Fetal Intestine Large	intestine
2	chr5:9134400-9156600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr5:9136800-9176400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:9136800-9189000	Weak transcription	Pancreas	Pancrea
5	chr5:9141200-9154400	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:9143600-9161000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:9145000-9154400	Weak transcription	Aorta	Aorta
8	chr5:9145000-9154400	Weak transcription	Liver	Liver
9	chr5:9145000-9154400	Weak transcription	Fetal Stomach	stomach
10	chr5:9145000-9158000	Weak transcription	Esophagus	oesophagus
11	chr5:9145200-9152200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr5:9145200-9157200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:9145200-9160800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:9145400-9163200	Weak transcription	Fetal Kidney	kidney
15	chr5:9145600-9235400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:9147600-9152600	Enhancers	NHDF-Ad	bronchial
17	chr5:9148600-9155600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:9148800-9153000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:9149800-9152400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:9150400-9156000	Weak transcription	Dnd41	blood
21	chr5:9150600-9154400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:9150800-9152400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr5:9150800-9153600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr5:9151000-9152600	Genic enhancers	NHLF	lung
25	chr5:9151000-9152800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:9151000-9169000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:9151200-9152200	Weak transcription	HMEC	breast
28	chr5:9151200-9153600	Weak transcription	Fetal Intestine Small	intestine
29	chr5:9151200-9154200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:9151200-9156400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:9151200-9168800	Weak transcription	NH-A	brain
32	chr5:9151600-9152800	Enhancers	Rectal Smooth Muscle	rectum
33	chr5:9151600-9157800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:9151800-9152400	Enhancers	Left Ventricle	heart
35	chr5:9151800-9153600	Enhancers	Colon Smooth Muscle	Colon
36	chr5:9151800-9153600	Enhancers	Fetal Heart	heart
37	chr5:9151800-9153800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:9151800-9154800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr5:9152000-9152200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr5:9152000-9152200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
41	chr5:9152000-9152400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr5:9152000-9152400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr5:9152000-9152400	ZNF genes & repeats	Lung	lung
44	chr5:9152000-9152400	Enhancers	Spleen	Spleen
45	chr5:9152000-9152600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:9152000-9152600	Enhancers	Right Ventricle	heart
47	chr5:9152000-9155200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr5:9152000-9155200	Strong transcription	Fetal Muscle Leg	muscle
49	chr5:9152000-9155400	Strong transcription	Cortex derived primary cultured neurospheres	brain

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