Variant report

Variant	rs7979919
Chromosome Location	chr12:12368983-12368984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12360154..12361666-chr12:12367455..12370218,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10082834	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083170	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10466847	1.00[ASN][1000 genomes]
rs10466848	1.00[ASN][1000 genomes]
rs10845497	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845499	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10845500	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054695	1.00[ASN][1000 genomes]
rs11054696	1.00[ASN][1000 genomes]
rs11054702	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054705	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054706	1.00[ASN][1000 genomes]
rs11054707	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054709	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054710	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054713	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11054720	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11054729	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11054732	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11054746	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054767	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1123213	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829211	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11831610	1.00[ASN][1000 genomes]
rs12296239	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12297598	0.90[EUR][1000 genomes]
rs12304957	0.83[EUR][1000 genomes]
rs12305378	1.00[ASN][1000 genomes]
rs12306293	1.00[ASN][1000 genomes]
rs12306537	1.00[ASN][1000 genomes]
rs12307111	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309246	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12309338	1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12310020	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12311202	1.00[ASN][1000 genomes]
rs12311922	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316043	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12319942	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12422890	1.00[ASN][1000 genomes]
rs12424332	1.00[ASN][1000 genomes]
rs12424361	1.00[ASN][1000 genomes]
rs12425185	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425699	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12427198	0.87[EUR][1000 genomes]
rs13377971	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16907789	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28448423	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56259928	1.00[ASN][1000 genomes]
rs56998126	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57055264	0.85[EUR][1000 genomes]
rs58682800	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59386755	1.00[ASN][1000 genomes]
rs7308022	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7311064	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061123	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74061145	0.90[EUR][1000 genomes]
rs7957531	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7960716	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7970975	0.82[YRI][hapmap]
rs7973583	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7973718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7978064	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9630249	1.00[ASN][1000 genomes]
rs9630250	1.00[ASN][1000 genomes]
rs9630266	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[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	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
rs7979919	LRP6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12315400-12371600	Weak transcription	Lung	lung
2	chr12:12336200-12369800	Weak transcription	Left Ventricle	heart
3	chr12:12336200-12381000	Weak transcription	Pancreas	Pancrea
4	chr12:12344200-12377000	Weak transcription	NHDF-Ad	bronchial
5	chr12:12354800-12370400	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:12355400-12369400	Weak transcription	Adipose Nuclei	Adipose
7	chr12:12355600-12369800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:12355800-12374200	Weak transcription	Fetal Intestine Large	intestine
9	chr12:12356000-12369000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:12356000-12370000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:12360800-12369000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:12360800-12374600	Weak transcription	Ovary	ovary
13	chr12:12361000-12369200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:12362200-12370000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:12364600-12370000	Weak transcription	GM12878-XiMat	blood
16	chr12:12366000-12369000	Weak transcription	Liver	Liver
17	chr12:12366400-12369200	Flanking Active TSS	A549	lung
18	chr12:12367600-12370400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:12367600-12370600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr12:12367600-12370600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:12367600-12371000	Enhancers	Primary hematopoietic stem cells	blood
22	chr12:12367800-12370200	Enhancers	Small Intestine	intestine
23	chr12:12367800-12372800	Weak transcription	Fetal Kidney	kidney
24	chr12:12367800-12375400	Enhancers	HepG2	liver
25	chr12:12368000-12369000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:12368000-12369000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:12368000-12369200	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:12368000-12369400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:12368000-12369800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr12:12368000-12369800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr12:12368000-12370400	Weak transcription	Colon Smooth Muscle	Colon
32	chr12:12368000-12373200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:12368000-12373800	Weak transcription	Fetal Lung	lung
34	chr12:12368200-12369000	Enhancers	K562	blood
35	chr12:12368200-12369200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr12:12368200-12369200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:12368200-12369200	Weak transcription	Brain Angular Gyrus	brain
38	chr12:12368200-12369200	Weak transcription	Stomach Mucosa	stomach
39	chr12:12368200-12369400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr12:12368200-12369400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:12368200-12369400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:12368200-12369800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:12368200-12369800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr12:12368200-12369800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:12368200-12369800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:12368200-12369800	Weak transcription	Brain Anterior Caudate	brain
47	chr12:12368200-12369800	Weak transcription	Brain Substantia Nigra	brain
48	chr12:12368200-12370400	Weak transcription	Primary T cells from cord blood	blood
49	chr12:12368200-12373200	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:12368200-12373800	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links