Variant report

Variant	rs7973583
Chromosome Location	chr12:12372787-12372788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10082834	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10083170	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466849	1.00[CHB][hapmap]
rs10845497	0.91[EUR][1000 genomes]
rs10845499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.81[EUR][1000 genomes]
rs11054702	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054705	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054707	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11054709	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs11054710	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs11054713	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs11054720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs11054765	1.00[CHB][hapmap]
rs11054767	1.00[JPT][hapmap]
rs11829211	0.81[EUR][1000 genomes]
rs12296239	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12297598	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12309246	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12309338	1.00[JPT][hapmap]
rs12310020	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12311922	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12316043	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs12319942	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422312	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs12425185	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12425699	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12425946	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs12427198	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16907789	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs28448423	0.91[EUR][1000 genomes]
rs56998126	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.89[EUR][1000 genomes]
rs7308022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74061123	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9630266	1.00[CEU][hapmap];1.00[JPT][hapmap]

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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1050715	chr12:12293072-12383820	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv832332	chr12:12344027-12484966	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7973583	LRP6	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
2	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
3	chr12:12355800-12374200	Weak transcription	Fetal Intestine Large	intestine
4	chr12:12360800-12374600	Weak transcription	Ovary	ovary
5	chr12:12367800-12372800	Weak transcription	Fetal Kidney	kidney
6	chr12:12367800-12375400	Enhancers	HepG2	liver
7	chr12:12368000-12373200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:12368000-12373800	Weak transcription	Fetal Lung	lung
9	chr12:12368200-12373200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:12368200-12373800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:12368200-12374400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:12368200-12374600	Weak transcription	HSMM	muscle
13	chr12:12368200-12376200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:12368200-12376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:12368200-12379000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:12368200-12381400	Weak transcription	Gastric	stomach
17	chr12:12368200-12384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:12368600-12381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:12368600-12381400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:12369200-12373800	Weak transcription	HSMMtube	muscle
22	chr12:12370200-12374400	Weak transcription	Small Intestine	intestine
23	chr12:12370400-12374600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:12370600-12373800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr12:12370600-12373800	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:12370600-12374000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:12370600-12374200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:12370600-12374200	Weak transcription	Brain Angular Gyrus	brain
29	chr12:12370600-12374200	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:12370600-12380800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:12370600-12381000	Weak transcription	Left Ventricle	heart
32	chr12:12370800-12373200	Weak transcription	K562	blood
33	chr12:12370800-12373800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:12370800-12374200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:12370800-12374600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:12370800-12379000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:12370800-12380800	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:12370800-12392200	Weak transcription	Brain Substantia Nigra	brain
39	chr12:12371000-12373800	Enhancers	A549	lung
40	chr12:12371000-12374000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:12371200-12376200	Weak transcription	Brain Anterior Caudate	brain
42	chr12:12371600-12374000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:12371600-12375200	Enhancers	Liver	Liver
44	chr12:12371800-12378200	Weak transcription	Fetal Muscle Leg	muscle
45	chr12:12372000-12376200	Weak transcription	GM12878-XiMat	blood
46	chr12:12372200-12376800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:12372400-12372800	Weak transcription	Lung	lung
48	chr12:12372600-12372800	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:12372600-12373000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr12:12372600-12374600	Enhancers	Brain Hippocampus Middle	brain

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