Variant report

Variant	rs3798036
Chromosome Location	chr5:9474363-9474364
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs16882852	0.85[CEU][hapmap]
rs169163	0.82[ASN][1000 genomes]
rs1700580	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs171992	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs198686	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs268469	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs268470	0.88[ASN][1000 genomes]
rs268471	0.87[ASN][1000 genomes]
rs268472	0.95[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs268473	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs268474	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs268476	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs268493	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs268494	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs268495	0.80[ASN][1000 genomes]
rs268496	0.82[ASN][1000 genomes]
rs268497	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs268498	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs268499	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs268500	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs268501	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs268503	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs268504	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs268508	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs268509	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs268517	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs268518	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs268519	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs268520	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs268521	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs268522	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs369459	0.86[CHB][hapmap]
rs377947	0.89[ASN][1000 genomes]
rs388157	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs389520	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs389537	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs399271	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs418373	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs418446	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs422556	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs432055	0.81[ASN][1000 genomes]
rs435128	0.87[ASN][1000 genomes]
rs438343	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs438506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs444808	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs446732	0.86[CHB][hapmap]
rs446904	0.89[ASN][1000 genomes]
rs486947	0.81[CHB][hapmap]
rs524976	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs645696	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs66526444	0.87[EUR][1000 genomes]
rs813717	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
3	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
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	esv3417107	chr5:9472102-9474800	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9437400-9477800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:9464800-9477400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr5:9465000-9477600	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:9468000-9477600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr5:9468400-9477200	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:9468600-9483000	Weak transcription	NHLF	lung
7	chr5:9469200-9479200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:9470400-9476600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:9470600-9482400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:9471200-9475400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:9471200-9477000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:9471400-9478000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:9471400-9480800	Weak transcription	Right Ventricle	heart
14	chr5:9472800-9476600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:9473600-9474400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:9473600-9474400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr5:9473600-9474400	Enhancers	Fetal Heart	heart
18	chr5:9473600-9475000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:9473600-9475000	Enhancers	NHDF-Ad	bronchial
20	chr5:9473800-9475000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:9474000-9475000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:9474000-9477800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:9474200-9474400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr5:9474200-9474800	Weak transcription	Left Ventricle	heart
25	chr5:9474200-9476600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:9474200-9477000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links