Variant report

Variant	rs3213566
Chromosome Location	chr12:121222578-121222579
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10774572	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10849791	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10849807	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11065264	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11065282	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs11065283	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs11065284	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11065292	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11065293	0.82[ASN][1000 genomes]
rs11065300	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11065311	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs11065324	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs1151849	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1151862	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11608262	0.82[ASN][1000 genomes]
rs11611087	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1177585	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12579868	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12580949	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs12809299	0.81[ASN][1000 genomes]
rs12822123	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12825746	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13746	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1467283	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1542859	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs1696357	0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs2015462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2047568	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2393717	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2893876	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs3213567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213570	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3213572	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs34076777	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35706672	0.82[ASN][1000 genomes]
rs3809313	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3842985	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3861797	0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3883901	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3897746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs3901854	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4454799	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs471688	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4766979	0.82[ASN][1000 genomes]
rs4767937	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs508595	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs520753	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs525425	0.96[ASN][1000 genomes]
rs531782	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs534415	0.96[ASN][1000 genomes]
rs572016	0.81[ASN][1000 genomes]
rs577961	0.81[ASN][1000 genomes]
rs580240	0.94[ASN][1000 genomes]
rs58291418	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs590625	0.81[ASN][1000 genomes]
rs608394	0.94[ASN][1000 genomes]
rs610694	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs618482	0.94[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs625228	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs661647	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs668622	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137504	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7305849	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs869781	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs909053	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9431	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs989986	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs989987	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs3213566	SPPL3	cis	cerebellum	SCAN
rs3213566	UNQ1887	cis	Frontal Cortex	GTEx
rs3213566	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs3213566	SRRM4	cis	cerebellum	SCAN
rs3213566	NOS1	cis	parietal	SCAN
rs3213566	UNQ1887	cis	Temporal Cortex	GTEx
rs3213566	UNC119B	cis	cerebellum	SCAN
rs3213566	SPPL3	cis	parietal	SCAN
rs3213566	SPPL3	cis	Nerve Tibial	GTEx
rs3213566	HPD	cis	parietal	SCAN
rs3213566	SPPL3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121200600-121222600	Strong transcription	Fetal Muscle Trunk	muscle
2	chr12:121206200-121238600	Weak transcription	Small Intestine	intestine
3	chr12:121207000-121223800	Weak transcription	Pancreas	Pancrea
4	chr12:121207200-121225000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:121207200-121226200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:121207200-121233000	Weak transcription	HSMMtube	muscle
7	chr12:121209200-121224200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:121209400-121236800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:121209800-121223400	Strong transcription	Fetal Thymus	thymus
10	chr12:121211400-121260800	Weak transcription	Gastric	stomach
11	chr12:121212600-121229600	Weak transcription	Right Atrium	heart
12	chr12:121212600-121229800	Weak transcription	Right Ventricle	heart
13	chr12:121212600-121236600	Weak transcription	Fetal Heart	heart
14	chr12:121212800-121228000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:121213200-121231200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:121213400-121224800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr12:121213600-121223000	Strong transcription	Dnd41	blood
18	chr12:121215000-121222800	Strong transcription	Liver	Liver
19	chr12:121215000-121224200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:121215200-121222800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr12:121215600-121222800	Strong transcription	Thymus	Thymus
22	chr12:121216400-121222800	Strong transcription	Fetal Intestine Large	intestine
23	chr12:121216800-121222800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:121216800-121222800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:121217000-121222800	Strong transcription	Fetal Muscle Leg	muscle
26	chr12:121217800-121222800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:121218000-121222600	Strong transcription	GM12878-XiMat	blood
28	chr12:121218200-121222600	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr12:121218200-121222800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:121218400-121222800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:121218600-121222600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:121218600-121222600	Strong transcription	Primary B cells from cord blood	blood
33	chr12:121218600-121222600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:121218600-121222600	Strong transcription	Brain Hippocampus Middle	brain
35	chr12:121218800-121222600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:121218800-121222800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:121219200-121222800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:121219400-121222600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:121219400-121222600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:121219400-121222600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr12:121219400-121222800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:121219600-121222600	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:121219600-121222600	Strong transcription	Adipose Nuclei	Adipose
44	chr12:121219600-121222600	Strong transcription	Aorta	Aorta
45	chr12:121219600-121222600	Strong transcription	Esophagus	oesophagus
46	chr12:121219600-121222800	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:121219800-121222600	Strong transcription	Fetal Brain Male	brain
48	chr12:121220000-121222600	Strong transcription	Fetal Kidney	kidney
49	chr12:121220200-121222600	Strong transcription	Rectal Smooth Muscle	rectum
50	chr12:121220400-121222600	Strong transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links