Variant report

Variant	rs12319942
Chromosome Location	chr12:12370595-12370596
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12369208..12371594-chr12:12405892..12408383,3	K562	blood:
2	chr12:12364652..12366406-chr12:12369471..12371207,2	K562	blood:
3	chr12:12364652..12367428-chr12:12369707..12372537,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10082834	0.85[EUR][1000 genomes]
rs10083170	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845497	0.96[EUR][1000 genomes]
rs10845499	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845500	0.87[EUR][1000 genomes]
rs11054720	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054729	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054732	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	0.92[EUR][1000 genomes]
rs11829211	0.83[EUR][1000 genomes]
rs12297598	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304957	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12311922	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12425185	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12427198	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448423	0.96[EUR][1000 genomes]
rs56998126	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055264	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	0.90[EUR][1000 genomes]
rs7308022	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74061123	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061145	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957531	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960716	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973583	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973718	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978064	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979919	0.82[AMR][1000 genomes];0.94[EUR][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	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
rs12319942	LRP6	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12315400-12371600	Weak transcription	Lung	lung
2	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
3	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
4	chr12:12355800-12374200	Weak transcription	Fetal Intestine Large	intestine
5	chr12:12360800-12374600	Weak transcription	Ovary	ovary
6	chr12:12367600-12370600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr12:12367600-12370600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:12367600-12371000	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:12367800-12372800	Weak transcription	Fetal Kidney	kidney
10	chr12:12367800-12375400	Enhancers	HepG2	liver
11	chr12:12368000-12373200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:12368000-12373800	Weak transcription	Fetal Lung	lung
13	chr12:12368200-12373200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:12368200-12373800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:12368200-12374400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:12368200-12374600	Weak transcription	HSMM	muscle
17	chr12:12368200-12376200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:12368200-12376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:12368200-12379000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:12368200-12381400	Weak transcription	Gastric	stomach
21	chr12:12368200-12384200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:12368400-12417200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:12368600-12381000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:12368600-12381400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:12368800-12370600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:12369000-12370600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:12369000-12370600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr12:12369000-12370800	Enhancers	Liver	Liver
29	chr12:12369000-12371600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:12369200-12370600	Enhancers	Brain Angular Gyrus	brain
31	chr12:12369200-12370800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:12369200-12370800	Enhancers	Brain Hippocampus Middle	brain
33	chr12:12369200-12373800	Weak transcription	HSMMtube	muscle
34	chr12:12369400-12370800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:12369400-12370800	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr12:12369400-12370800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr12:12369600-12370600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr12:12369800-12370600	Enhancers	H1 Cell Line	embryonic stem cell
39	chr12:12369800-12370600	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr12:12369800-12370600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:12369800-12370600	Enhancers	Brain Anterior Caudate	brain
42	chr12:12369800-12370600	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr12:12369800-12370600	Enhancers	Left Ventricle	heart
44	chr12:12369800-12370800	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr12:12369800-12370800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:12369800-12370800	Enhancers	Brain Cingulate Gyrus	brain
47	chr12:12369800-12370800	Enhancers	Brain Substantia Nigra	brain
48	chr12:12370000-12370600	Enhancers	Psoas Muscle	Psoas
49	chr12:12370000-12372000	Enhancers	GM12878-XiMat	blood
50	chr12:12370200-12370800	Enhancers	K562	blood

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