Variant report

Variant	rs253653
Chromosome Location	chr5:9114271-9114272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12519438	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1479648	0.87[ASN][1000 genomes]
rs168817	0.87[EUR][1000 genomes]
rs190423	0.87[ASN][1000 genomes]
rs1904454	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2456237	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs253633	0.88[EUR][1000 genomes]
rs253635	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs253636	0.89[EUR][1000 genomes]
rs253639	0.89[EUR][1000 genomes]
rs253645	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs253646	0.88[EUR][1000 genomes]
rs253647	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs253648	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253649	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253652	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253660	0.87[ASN][1000 genomes]
rs6862429	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6876444	0.87[ASN][1000 genomes]
rs9313270	0.80[ASN][1000 genomes]
rs975096	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs990679	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9040800-9122000	Weak transcription	Colonic Mucosa	Colon
2	chr5:9065400-9115800	Weak transcription	Aorta	Aorta
3	chr5:9086200-9115000	Weak transcription	Fetal Intestine Small	intestine
4	chr5:9092800-9115000	Weak transcription	Fetal Heart	heart
5	chr5:9094200-9115000	Weak transcription	Pancreas	Pancrea
6	chr5:9105000-9119000	Weak transcription	Spleen	Spleen
7	chr5:9105200-9120400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr5:9105200-9145000	Weak transcription	Osteobl	bone
9	chr5:9105400-9115600	Weak transcription	Fetal Lung	lung
10	chr5:9105400-9118600	Weak transcription	Fetal Stomach	stomach
11	chr5:9108000-9123200	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:9108400-9115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:9108400-9118800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:9108400-9135800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:9108600-9115000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:9108600-9115000	Weak transcription	Fetal Muscle Leg	muscle
17	chr5:9108600-9115200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:9108600-9115600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:9108600-9118600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr5:9108600-9118600	Weak transcription	Right Ventricle	heart
21	chr5:9108600-9119000	Weak transcription	Fetal Intestine Large	intestine
22	chr5:9108600-9131800	Weak transcription	NHLF	lung
23	chr5:9108800-9115000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr5:9108800-9115600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:9108800-9147600	Weak transcription	NHDF-Ad	bronchial
26	chr5:9110000-9115000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:9110800-9114600	Weak transcription	Liver	Liver
28	chr5:9110800-9115600	Weak transcription	Left Ventricle	heart
29	chr5:9111000-9118400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:9111200-9115200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr5:9111400-9114800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:9112200-9114600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:9112600-9117200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:9112800-9119400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:9112800-9126800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:9113200-9118800	Weak transcription	Esophagus	oesophagus
37	chr5:9113400-9116200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr5:9113600-9114600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:9113600-9118600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:9113800-9116200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:9114000-9115000	ZNF genes & repeats	Fetal Kidney	kidney
42	chr5:9114000-9119200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:9114200-9114400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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