Variant report

Variant	rs1854441
Chromosome Location	chr9:79266721-79266722
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10521475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11144986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11144987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs11144992	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11144996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17062768	1.00[CEU][hapmap]
rs17062772	1.00[CEU][hapmap]
rs17062775	1.00[CEU][hapmap]
rs17062778	1.00[CEU][hapmap]
rs17062858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1952460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs2067501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs499746	1.00[CEU][hapmap]
rs57389265	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs634063	0.93[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs637207	1.00[CEU][hapmap]
rs644893	1.00[CEU][hapmap]
rs7027074	0.95[ASN][1000 genomes]
rs7028756	0.91[ASN][1000 genomes]
rs7038619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs7039310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7045505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs7847922	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7859873	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79252600-79278000	Weak transcription	Gastric	stomach
2	chr9:79258000-79270000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:79258200-79267800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:79259000-79269200	Weak transcription	Brain Substantia Nigra	brain
5	chr9:79259000-79278000	Weak transcription	Spleen	Spleen
6	chr9:79260000-79282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:79263600-79267000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr9:79263600-79268600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:79263600-79268600	Weak transcription	Aorta	Aorta
10	chr9:79263600-79272800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:79263600-79282200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:79264000-79267200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr9:79264800-79267200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:79265200-79267600	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr9:79265400-79266800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:79265400-79267000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:79265400-79267400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr9:79265400-79267400	Enhancers	Fetal Intestine Large	intestine
19	chr9:79265400-79267600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr9:79265400-79267600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:79265400-79267600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr9:79265400-79267800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr9:79265400-79268200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr9:79265400-79268600	Enhancers	Muscle Satellite Cultured Cells	--
25	chr9:79265400-79269200	Genic enhancers	HSMM	muscle
26	chr9:79265400-79270800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr9:79265600-79266800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:79265600-79266800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:79265600-79266800	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr9:79265600-79267000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr9:79265600-79267400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr9:79265600-79267400	Enhancers	Small Intestine	intestine
33	chr9:79265600-79267600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:79265600-79267600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr9:79265600-79268000	Enhancers	Colon Smooth Muscle	Colon
36	chr9:79265600-79268200	Enhancers	GM12878-XiMat	blood
37	chr9:79265600-79268400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr9:79265600-79269600	Weak transcription	Brain Angular Gyrus	brain
39	chr9:79265600-79270600	Enhancers	Fetal Thymus	thymus
40	chr9:79265600-79270600	Enhancers	NHLF	lung
41	chr9:79265600-79274000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:79265800-79266800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr9:79265800-79266800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr9:79265800-79266800	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr9:79265800-79266800	Active TSS	Rectal Smooth Muscle	rectum
46	chr9:79265800-79266800	Flanking Active TSS	HUVEC	blood vessel
47	chr9:79265800-79267200	Enhancers	Liver	Liver
48	chr9:79265800-79268800	Weak transcription	Fetal Heart	heart
49	chr9:79266000-79266800	Active TSS	Ovary	ovary
50	chr9:79266000-79266800	Active TSS	Right Atrium	heart

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