Variant report

Variant	rs12875311
Chromosome Location	chr13:40342557-40342558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11618582	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12872801	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12876235	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28635831	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34394770	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4514547	0.82[GIH][hapmap]
rs4569133	0.82[GIH][hapmap]
rs7319041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320598	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7986796	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7989997	0.83[AFR][1000 genomes]
rs7991151	0.82[GIH][hapmap]
rs7993214	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7994665	0.81[CHB][hapmap]
rs8002731	1.00[CEU][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9532430	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9532433	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9532434	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9548895	0.81[CHB][hapmap]
rs9548932	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9594366	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9603603	0.96[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9603605	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9603608	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9603610	0.83[AFR][1000 genomes]
rs9603611	0.83[AFR][1000 genomes]
rs9603612	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9603616	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9943	1.00[ASW][hapmap];0.92[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv471130	chr13:40261945-40350912	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12875311	LOC646982	cis	parietal	SCAN
rs12875311	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40311400-40347200	Weak transcription	HSMM	muscle
2	chr13:40312200-40351200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:40327400-40344400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:40327400-40352200	Weak transcription	Primary T cells from cord blood	blood
5	chr13:40327800-40347400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr13:40330000-40345200	Weak transcription	Aorta	Aorta
7	chr13:40339200-40342600	Enhancers	Fetal Brain Male	brain
8	chr13:40339200-40342800	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr13:40339400-40342600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:40339400-40342600	Enhancers	Adipose Nuclei	Adipose
11	chr13:40339400-40342800	Enhancers	Fetal Brain Female	brain
12	chr13:40339600-40343200	Enhancers	Brain Germinal Matrix	brain
13	chr13:40339800-40342600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr13:40339800-40342600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr13:40339800-40342600	Enhancers	Brain Anterior Caudate	brain
16	chr13:40339800-40343200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr13:40340000-40342600	Enhancers	Fetal Muscle Leg	muscle
18	chr13:40340000-40343000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:40340400-40347000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr13:40340400-40347800	Weak transcription	HUVEC	blood vessel
21	chr13:40340400-40353600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:40340400-40361200	Weak transcription	Pancreas	Pancrea
23	chr13:40340600-40345800	Weak transcription	Left Ventricle	heart
24	chr13:40340600-40351200	Weak transcription	Gastric	stomach
25	chr13:40340600-40351200	Weak transcription	Right Ventricle	heart
26	chr13:40341000-40344200	Weak transcription	Liver	Liver
27	chr13:40341000-40346800	Weak transcription	Fetal Stomach	stomach
28	chr13:40341200-40342800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr13:40341200-40343000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr13:40341200-40343200	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr13:40341400-40350600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr13:40341800-40342600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr13:40341800-40342600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr13:40341800-40342600	Enhancers	Fetal Muscle Trunk	muscle
35	chr13:40341800-40342800	Enhancers	Primary B cells from peripheral blood	blood
36	chr13:40341800-40342800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr13:40341800-40342800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr13:40341800-40342800	Enhancers	Esophagus	oesophagus
39	chr13:40341800-40342800	Enhancers	Psoas Muscle	Psoas
40	chr13:40341800-40343000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr13:40341800-40356600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr13:40342000-40342800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr13:40342200-40342600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr13:40342200-40343400	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr13:40342200-40343400	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr13:40342200-40348000	Weak transcription	Ovary	ovary
47	chr13:40342400-40342600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:40342400-40342600	Enhancers	Brain Cingulate Gyrus	brain
49	chr13:40342400-40342600	Enhancers	Fetal Lung	lung
50	chr13:40342400-40342600	Enhancers	Lung	lung

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