Variant report

Variant	rs989987
Chromosome Location	chr12:121274062-121274063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:121273818-121274259	T-47D	breast:	n/a	n/a
2	GATA3	chr12:121273802-121274320	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121163485..121165709-chr12:121272071..121274503,2	MCF-7	breast:
2	chr12:121273900..121276013-chr12:121279474..121281086,2	MCF-7	breast:

Variant related genes	Relation type
SPPL3	TF binding region
ENSG00000122971	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10774572	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10849791	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10849807	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065264	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11065282	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065283	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065284	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065292	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065293	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065300	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11065307	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065311	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1151849	0.81[ASN][1000 genomes]
rs1151859	0.82[ASN][1000 genomes]
rs1151862	0.82[ASN][1000 genomes]
rs11608262	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11611087	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168944	0.83[ASN][1000 genomes]
rs1168946	0.83[ASN][1000 genomes]
rs1168948	0.83[ASN][1000 genomes]
rs1168953	0.83[ASN][1000 genomes]
rs1177585	0.83[ASN][1000 genomes]
rs1179939	0.83[ASN][1000 genomes]
rs12371178	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12579868	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12580949	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12809299	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12822123	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12825746	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12831094	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1467283	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1542859	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2015462	0.83[ASN][1000 genomes]
rs2047568	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2393717	0.82[ASN][1000 genomes]
rs2461475	0.95[ASN][1000 genomes]
rs2650017	0.83[ASN][1000 genomes]
rs2893876	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213566	0.82[ASN][1000 genomes]
rs3213567	0.82[ASN][1000 genomes]
rs3213570	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3213572	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34009825	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34076777	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35706672	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35905305	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3809313	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3842985	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3861797	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3883901	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3897746	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3901854	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4454799	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs471688	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766979	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766980	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4767937	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs487943	0.85[ASN][1000 genomes]
rs494632	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs520753	0.84[ASN][1000 genomes]
rs525425	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs531782	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs533264	0.84[ASN][1000 genomes]
rs534415	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs548452	0.85[ASN][1000 genomes]
rs572016	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577961	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58291418	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58918988	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs590625	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs602984	0.83[ASN][1000 genomes]
rs609700	0.84[ASN][1000 genomes]
rs610694	0.84[ASN][1000 genomes]
rs624216	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625228	0.98[ASN][1000 genomes]
rs647881	0.84[ASN][1000 genomes]
rs661647	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs665585	0.85[ASN][1000 genomes]
rs666976	0.83[ASN][1000 genomes]
rs7137504	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7305849	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73413868	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7969140	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs869781	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs909053	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9431	0.80[ASN][1000 genomes]
rs989986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs989987	ACADS	cis	Thyroid	GTEx
rs989987	SPPL3	cis	Adipose Subcutaneous	GTEx
rs989987	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs989987	SPPL3	cis	Nerve Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121261600-121274400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr12:121264800-121275000	Enhancers	Brain Hippocampus Middle	brain
3	chr12:121265400-121274200	Enhancers	Brain Angular Gyrus	brain
4	chr12:121266000-121274200	Enhancers	Brain Cingulate Gyrus	brain
5	chr12:121266400-121274600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:121266800-121276200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr12:121267200-121282800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:121267600-121285800	Weak transcription	Colonic Mucosa	Colon
9	chr12:121267800-121274800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr12:121268400-121274800	Enhancers	Rectal Smooth Muscle	rectum
11	chr12:121268600-121274200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:121268600-121274600	Enhancers	Adipose Nuclei	Adipose
13	chr12:121268600-121274600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr12:121268600-121274800	Enhancers	Colon Smooth Muscle	Colon
15	chr12:121268600-121276200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:121268600-121276600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr12:121269000-121278400	Weak transcription	Ovary	ovary
18	chr12:121269200-121274200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:121269600-121274200	Weak transcription	Liver	Liver
20	chr12:121269800-121281200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:121269800-121281200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:121269800-121282800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:121269800-121291400	Weak transcription	Fetal Intestine Large	intestine
24	chr12:121270200-121274800	Enhancers	Fetal Thymus	thymus
25	chr12:121270200-121274800	Enhancers	Thymus	Thymus
26	chr12:121270400-121274400	Enhancers	Primary B cells from cord blood	blood
27	chr12:121270600-121275200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr12:121270800-121274200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr12:121270800-121274800	Enhancers	Primary B cells from peripheral blood	blood
30	chr12:121271000-121274200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:121271000-121274400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:121271000-121274400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr12:121271000-121274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr12:121271000-121275000	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr12:121271200-121274400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:121271200-121274400	Enhancers	Primary hematopoietic stem cells	blood
37	chr12:121271200-121274400	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr12:121271200-121278400	Weak transcription	Fetal Intestine Small	intestine
39	chr12:121271400-121274200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:121271600-121274600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr12:121271600-121274600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:121271600-121274800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr12:121271800-121274200	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr12:121271800-121274400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:121271800-121274400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:121271800-121274400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr12:121271800-121274800	Enhancers	Dnd41	blood
48	chr12:121272000-121274200	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr12:121272000-121274400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr12:121272200-121274200	Weak transcription	Duodenum Mucosa	Duodenum

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