Variant report

Variant	rs253652
Chromosome Location	chr5:9115267-9115268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12189232	0.85[CEU][hapmap]
rs12519438	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1479648	0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs168817	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs1806097	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs190423	0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1904454	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2256569	0.81[CHB][hapmap]
rs2456237	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs2526121	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs2526122	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs253633	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs253634	0.85[CEU][hapmap]
rs253635	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs253636	0.89[EUR][1000 genomes]
rs253638	0.85[CEU][hapmap]
rs253639	0.89[EUR][1000 genomes]
rs253644	0.83[CEU][hapmap]
rs253645	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs253646	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs253647	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs253648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs253653	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	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6863413	0.89[CEU][hapmap]
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]
rs988593	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs990679	0.89[JPT][hapmap];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:45 , 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	chr5:9105000-9119000	Weak transcription	Spleen	Spleen
4	chr5:9105200-9120400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr5:9105200-9145000	Weak transcription	Osteobl	bone
6	chr5:9105400-9115600	Weak transcription	Fetal Lung	lung
7	chr5:9105400-9118600	Weak transcription	Fetal Stomach	stomach
8	chr5:9108000-9123200	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:9108400-9118800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:9108400-9135800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr5:9108600-9115600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:9108600-9118600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:9108600-9118600	Weak transcription	Right Ventricle	heart
14	chr5:9108600-9119000	Weak transcription	Fetal Intestine Large	intestine
15	chr5:9108600-9131800	Weak transcription	NHLF	lung
16	chr5:9108800-9115600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:9108800-9147600	Weak transcription	NHDF-Ad	bronchial
18	chr5:9110800-9115600	Weak transcription	Left Ventricle	heart
19	chr5:9111000-9118400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr5:9112600-9117200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:9112800-9119400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:9112800-9126800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:9113200-9118800	Weak transcription	Esophagus	oesophagus
24	chr5:9113400-9116200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr5:9113600-9118600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr5:9113800-9116200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr5:9114000-9119200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:9114600-9116400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr5:9114600-9117400	Strong transcription	Liver	Liver
30	chr5:9114800-9116000	Enhancers	Dnd41	blood
31	chr5:9114800-9119200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:9115000-9115400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:9115000-9115600	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr5:9115000-9115800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:9115000-9116000	Strong transcription	Fetal Kidney	kidney
36	chr5:9115000-9116200	Strong transcription	Pancreas	Pancrea
37	chr5:9115000-9116400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:9115000-9116400	Strong transcription	Fetal Muscle Leg	muscle
39	chr5:9115000-9116600	Strong transcription	Fetal Muscle Trunk	muscle
40	chr5:9115000-9117600	Strong transcription	Fetal Heart	heart
41	chr5:9115000-9123200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr5:9115200-9116000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:9115200-9116400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:9115200-9116400	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr5:9115200-9119400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links