Variant report

Variant	rs12831094
Chromosome Location	chr12:121292704-121292705
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121243655..121245803-chr12:121292539..121295448,2	MCF-7	breast:
2	chr12:121291111..121293734-chr12:121317316..121319397,2	K562	blood:
3	chr12:121292231..121294396-chr12:121341344..121344172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10774572	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849791	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10849807	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065282	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065283	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065284	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065292	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065293	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065300	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065307	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065311	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065324	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065332	0.81[ASN][1000 genomes]
rs1151849	0.90[ASN][1000 genomes]
rs1151859	0.91[ASN][1000 genomes]
rs1151862	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11608262	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11611087	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1168944	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168946	0.92[ASN][1000 genomes]
rs1168948	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168953	0.92[ASN][1000 genomes]
rs1177585	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1179939	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12371178	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12372231	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12580949	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809299	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12822123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12825746	0.84[ASN][1000 genomes]
rs1542859	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1696357	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1696390	0.83[ASN][1000 genomes]
rs1718188	0.84[ASN][1000 genomes]
rs2047568	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2393716	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2461475	0.80[ASN][1000 genomes]
rs2650017	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701177	0.84[ASN][1000 genomes]
rs2701184	0.86[ASN][1000 genomes]
rs2893876	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3213572	0.82[AMR][1000 genomes]
rs34009825	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34076777	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35600816	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35706672	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35905305	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3809313	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3842985	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3861797	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3883901	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3897746	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4454799	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471688	0.84[ASN][1000 genomes]
rs4766979	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4766980	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767937	0.82[AMR][1000 genomes]
rs4767941	0.85[ASN][1000 genomes]
rs487943	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs520753	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531782	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs533264	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs548452	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs572016	0.84[ASN][1000 genomes]
rs577961	0.84[ASN][1000 genomes]
rs58291418	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58918988	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs590625	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs602984	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs609700	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610694	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61946382	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61946383	0.83[ASN][1000 genomes]
rs61946384	0.84[ASN][1000 genomes]
rs61946385	0.83[ASN][1000 genomes]
rs61946386	0.83[ASN][1000 genomes]
rs624216	0.84[ASN][1000 genomes]
rs625228	0.83[ASN][1000 genomes]
rs647881	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs661647	0.84[ASN][1000 genomes]
rs665585	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs666976	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73413868	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73415720	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73415734	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7969140	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980311	0.86[ASN][1000 genomes]
rs869781	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs909053	0.82[AMR][1000 genomes]
rs989986	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs989987	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12831094	SPPL3	cis	Adipose Subcutaneous	GTEx
rs12831094	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs12831094	SPPL3	cis	Nerve Tibial	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121281600-121296200	Weak transcription	HepG2	liver
2	chr12:121282000-121308600	Weak transcription	Fetal Kidney	kidney
3	chr12:121283200-121310200	Weak transcription	Placenta	Placenta
4	chr12:121283400-121307400	Weak transcription	Esophagus	oesophagus
5	chr12:121283600-121295600	Weak transcription	Fetal Stomach	stomach
6	chr12:121283600-121302200	Weak transcription	Lung	lung
7	chr12:121284000-121294400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:121284600-121292800	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:121286400-121293800	Weak transcription	Right Ventricle	heart
10	chr12:121286600-121293600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:121287600-121293400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:121287600-121294000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:121287800-121300400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:121288000-121292800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:121288000-121293400	Weak transcription	Brain Substantia Nigra	brain
16	chr12:121288000-121294400	Weak transcription	Right Atrium	heart
17	chr12:121288000-121294600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:121288000-121300200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:121288000-121311800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:121288000-121316600	Weak transcription	NHLF	lung
21	chr12:121288200-121293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
23	chr12:121288600-121292800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:121288600-121293800	Weak transcription	HSMM	muscle
25	chr12:121289800-121293600	Weak transcription	Brain Anterior Caudate	brain
26	chr12:121289800-121294400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:121289800-121294600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr12:121289800-121296000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:121289800-121297800	Weak transcription	Ovary	ovary
30	chr12:121290000-121293400	Weak transcription	Fetal Muscle Leg	muscle
31	chr12:121290000-121293600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:121290000-121300200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:121290000-121302600	Weak transcription	Liver	Liver
34	chr12:121290600-121293000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr12:121290800-121294200	Enhancers	Left Ventricle	heart
36	chr12:121290800-121295200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:121290800-121295800	Enhancers	Fetal Thymus	thymus
38	chr12:121291000-121293000	Enhancers	Primary hematopoietic stem cells	blood
39	chr12:121291000-121295000	Enhancers	Adipose Nuclei	Adipose
40	chr12:121291000-121295400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:121291000-121295600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr12:121291000-121296400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr12:121291200-121295000	Enhancers	Colon Smooth Muscle	Colon
44	chr12:121291200-121295200	Enhancers	Primary T cells from cord blood	blood
45	chr12:121291200-121296200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:121291400-121292800	Enhancers	Small Intestine	intestine
47	chr12:121291400-121293000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:121291400-121293200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr12:121291400-121295000	Enhancers	Brain Cingulate Gyrus	brain
50	chr12:121291400-121295600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links