Variant report

Variant	rs602984
Chromosome Location	chr12:121293228-121293229
allele	C/G
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	chr12:121293123..121296169-chr12:121296958..121300717,3	MCF-7	breast:
3	chr12:121291111..121293734-chr12:121317316..121319397,2	K562	blood:
4	chr12:121292231..121294396-chr12:121341344..121344172,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10774572	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10849807	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11065282	0.83[ASN][1000 genomes]
rs11065283	0.83[ASN][1000 genomes]
rs11065284	0.83[ASN][1000 genomes]
rs11065292	0.83[ASN][1000 genomes]
rs11065293	0.83[ASN][1000 genomes]
rs11065300	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11065307	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065311	0.91[ASN][1000 genomes]
rs11065324	0.84[ASN][1000 genomes]
rs1151849	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1151859	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1151862	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11608262	0.82[ASN][1000 genomes]
rs11611087	0.83[ASN][1000 genomes]
rs1168944	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168946	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168948	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168953	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1177585	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1179939	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12371178	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12372231	0.85[ASN][1000 genomes]
rs12580949	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12809299	0.83[ASN][1000 genomes]
rs12822123	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12825746	0.83[ASN][1000 genomes]
rs12831094	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13746	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1542859	0.91[ASN][1000 genomes]
rs1696357	0.85[ASN][1000 genomes]
rs1696390	0.83[ASN][1000 genomes]
rs1718180	0.82[EUR][1000 genomes]
rs1718188	0.85[ASN][1000 genomes]
rs2461475	0.81[ASN][1000 genomes]
rs2650017	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2701177	0.85[ASN][1000 genomes]
rs2701184	0.84[ASN][1000 genomes]
rs34009825	0.91[ASN][1000 genomes]
rs34076777	0.83[ASN][1000 genomes]
rs35600816	0.86[ASN][1000 genomes]
rs35706672	0.83[ASN][1000 genomes]
rs35905305	0.90[ASN][1000 genomes]
rs3809313	0.91[ASN][1000 genomes]
rs3842985	0.80[ASN][1000 genomes]
rs3861797	0.80[ASN][1000 genomes]
rs3883901	0.80[ASN][1000 genomes]
rs3897746	0.91[ASN][1000 genomes]
rs4454799	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs471688	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4766979	0.83[ASN][1000 genomes]
rs4766980	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4767941	0.83[ASN][1000 genomes]
rs487943	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs508595	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs520753	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs531782	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs533264	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs548452	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs572016	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs577961	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs580240	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58291418	0.83[ASN][1000 genomes]
rs58918988	0.90[ASN][1000 genomes]
rs590625	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs609700	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs610694	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs618482	0.81[AMR][1000 genomes]
rs61946382	0.84[ASN][1000 genomes]
rs61946383	0.81[ASN][1000 genomes]
rs61946384	0.83[ASN][1000 genomes]
rs61946385	0.81[ASN][1000 genomes]
rs61946386	0.81[ASN][1000 genomes]
rs624216	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs625228	0.84[ASN][1000 genomes]
rs647881	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs661647	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs665585	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs666976	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73413868	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73415720	0.84[ASN][1000 genomes]
rs73415734	0.81[ASN][1000 genomes]
rs7969140	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7980311	0.84[ASN][1000 genomes]
rs869781	0.90[ASN][1000 genomes]
rs9431	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs989986	0.83[ASN][1000 genomes]
rs989987	0.83[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs602984	SPPL3	cis	Adipose Subcutaneous	GTEx
rs602984	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL

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	chr12:121286400-121293800	Weak transcription	Right Ventricle	heart
9	chr12:121286600-121293600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:121287600-121293400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:121287600-121294000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:121287800-121300400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:121288000-121293400	Weak transcription	Brain Substantia Nigra	brain
14	chr12:121288000-121294400	Weak transcription	Right Atrium	heart
15	chr12:121288000-121294600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:121288000-121300200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:121288000-121311800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:121288000-121316600	Weak transcription	NHLF	lung
19	chr12:121288200-121293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
21	chr12:121288600-121293800	Weak transcription	HSMM	muscle
22	chr12:121289800-121293600	Weak transcription	Brain Anterior Caudate	brain
23	chr12:121289800-121294400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:121289800-121294600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:121289800-121296000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr12:121289800-121297800	Weak transcription	Ovary	ovary
27	chr12:121290000-121293400	Weak transcription	Fetal Muscle Leg	muscle
28	chr12:121290000-121293600	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr12:121290000-121300200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:121290000-121302600	Weak transcription	Liver	Liver
31	chr12:121290800-121294200	Enhancers	Left Ventricle	heart
32	chr12:121290800-121295200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:121290800-121295800	Enhancers	Fetal Thymus	thymus
34	chr12:121291000-121295000	Enhancers	Adipose Nuclei	Adipose
35	chr12:121291000-121295400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:121291000-121295600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr12:121291000-121296400	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr12:121291200-121295000	Enhancers	Colon Smooth Muscle	Colon
39	chr12:121291200-121295200	Enhancers	Primary T cells from cord blood	blood
40	chr12:121291200-121296200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:121291400-121295000	Enhancers	Brain Cingulate Gyrus	brain
42	chr12:121291400-121295600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr12:121291400-121295600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr12:121291600-121293600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:121291600-121293600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:121291600-121294000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr12:121291600-121295200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:121291600-121295800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr12:121291600-121296000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:121291600-121296200	Weak transcription	A549	lung

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