Variant report

Variant	rs9521747
Chromosome Location	chr13:111060205-111060206
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11619425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11619427	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11619430	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1927343	0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1927344	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1927345	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1927346	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1927347	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1927349	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2149067	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35843316	0.82[EUR][1000 genomes]
rs3899318	0.80[EUR][1000 genomes]
rs4492912	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4547215	0.87[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4771675	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4771676	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7321362	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7323228	0.87[CHB][hapmap];0.86[CHD][hapmap];0.85[MEX][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7982993	0.87[CHB][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7990844	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9284253	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9301454	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9515204	0.84[EUR][1000 genomes]
rs9521740	0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9521742	0.84[EUR][1000 genomes]
rs9521744	0.82[EUR][1000 genomes]
rs9521746	0.87[CHB][hapmap];0.84[EUR][1000 genomes]
rs9521748	0.84[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2751128	chr13:111040798-111132490	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3354806	chr13:111059151-111063549	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9521747	COL4A2	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111050200-111064400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr13:111050200-111066000	Enhancers	NHDF-Ad	bronchial
3	chr13:111050200-111075200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:111050400-111060400	Enhancers	HSMMtube	muscle
5	chr13:111052200-111063400	Weak transcription	Psoas Muscle	Psoas
6	chr13:111053000-111063600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:111054600-111061200	Enhancers	NH-A	brain
8	chr13:111054800-111060400	Enhancers	NHLF	lung
9	chr13:111056200-111060800	Enhancers	Left Ventricle	heart
10	chr13:111056200-111066000	Enhancers	Lung	lung
11	chr13:111056400-111060400	Enhancers	Colon Smooth Muscle	Colon
12	chr13:111057000-111061200	Enhancers	Fetal Heart	heart
13	chr13:111057400-111061600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr13:111057600-111060400	Weak transcription	NHEK	skin
15	chr13:111057800-111064800	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr13:111057800-111070400	Enhancers	Right Atrium	heart
17	chr13:111058000-111060400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:111058000-111061200	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr13:111058000-111066000	Enhancers	HUVEC	blood vessel
20	chr13:111058200-111060600	Enhancers	Fetal Lung	lung
21	chr13:111058200-111062200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:111058400-111060400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr13:111058400-111062400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr13:111058400-111062800	Strong transcription	Fetal Intestine Small	intestine
25	chr13:111058600-111060400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr13:111058600-111061000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr13:111058600-111061000	Weak transcription	Fetal Kidney	kidney
28	chr13:111058600-111061600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr13:111058600-111062000	Genic enhancers	Fetal Muscle Trunk	muscle
30	chr13:111058800-111060400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:111058800-111063600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr13:111058800-111063800	Weak transcription	Small Intestine	intestine
33	chr13:111058800-111064200	Weak transcription	Fetal Intestine Large	intestine
34	chr13:111059000-111063200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:111059200-111060400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
36	chr13:111059200-111063600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr13:111059400-111060400	Weak transcription	HSMM	muscle
38	chr13:111059400-111061000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr13:111059400-111061000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:111059400-111062600	Genic enhancers	Fetal Muscle Leg	muscle
41	chr13:111059400-111063800	Genic enhancers	Fetal Stomach	stomach
42	chr13:111059400-111065200	Enhancers	Spleen	Spleen
43	chr13:111059400-111067000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:111059600-111060400	Enhancers	Brain Hippocampus Middle	brain
45	chr13:111059600-111060800	Bivalent Enhancer	Fetal Thymus	thymus
46	chr13:111059600-111061000	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr13:111059600-111061400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr13:111059600-111061600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr13:111059600-111062000	Genic enhancers	Muscle Satellite Cultured Cells	--
50	chr13:111059600-111064200	Genic enhancers	Osteobl	bone

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