Variant report

Variant	rs6149
Chromosome Location	chr9:2635545-2635546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10812377	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10812378	0.82[ASW][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10812379	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10967260	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12336893	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12336931	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3780181	0.82[MKK][hapmap];0.93[YRI][hapmap]
rs7035616	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[ASN][1000 genomes]
rs7044155	0.85[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6149	WNT3A	trans	lymphoblastoid	seeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2623800-2641000	Weak transcription	Esophagus	oesophagus
2	chr9:2624000-2636000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:2624200-2635600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:2624200-2636000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:2624200-2641000	Weak transcription	Aorta	Aorta
6	chr9:2624400-2641200	Weak transcription	Fetal Kidney	kidney
7	chr9:2624400-2643000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:2624400-2643200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:2624800-2636000	Weak transcription	A549	lung
10	chr9:2625000-2641000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:2627200-2648400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:2630600-2638000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr9:2630600-2639800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:2630600-2641000	Weak transcription	Gastric	stomach
15	chr9:2630600-2641200	Weak transcription	Lung	lung
16	chr9:2632000-2635600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:2632600-2635600	Enhancers	Brain Angular Gyrus	brain
18	chr9:2632600-2635800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:2633000-2635600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr9:2633000-2639800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:2633200-2643200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:2633200-2646000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:2633400-2640000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:2633600-2656600	Weak transcription	Colon Smooth Muscle	Colon
25	chr9:2634000-2643000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr9:2634000-2645000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:2634200-2645400	Weak transcription	HSMMtube	muscle
28	chr9:2634400-2638600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr9:2634400-2639400	Weak transcription	Fetal Brain Male	brain
30	chr9:2634400-2639800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr9:2634400-2641000	Weak transcription	Right Ventricle	heart
32	chr9:2634400-2648200	Weak transcription	Placenta	Placenta
33	chr9:2634600-2635800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:2634600-2636000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:2634600-2636000	Weak transcription	Fetal Brain Female	brain
36	chr9:2634600-2636000	Weak transcription	Ovary	ovary
37	chr9:2634600-2636200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr9:2634600-2639000	Weak transcription	Pancreas	Pancrea
39	chr9:2634600-2639200	Weak transcription	Right Atrium	heart
40	chr9:2634600-2643200	Weak transcription	NHLF	lung
41	chr9:2634800-2636000	Weak transcription	Stomach Smooth Muscle	stomach
42	chr9:2634800-2636200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr9:2634800-2636600	Enhancers	Brain Cingulate Gyrus	brain
44	chr9:2634800-2636800	Enhancers	Brain Hippocampus Middle	brain
45	chr9:2634800-2637400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr9:2634800-2637400	Enhancers	Brain Anterior Caudate	brain
47	chr9:2634800-2638600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr9:2634800-2643400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr9:2635000-2636800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:2635000-2643200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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