Variant report

Variant	rs989986
Chromosome Location	chr12:121274178-121274179
allele	G/T
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: 97 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10774572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10849791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10849807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11065324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1151849	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs1151859	0.82[ASN][1000 genomes]
rs1151862	1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];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	1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12824150	0.85[CEU][hapmap]
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]
rs13746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs1467283	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1542859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1696357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2015462	0.83[ASN][1000 genomes]
rs2047568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2062507	0.85[CEU][hapmap]
rs2393717	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	0.95[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]
rs3213567	0.82[ASN][1000 genomes]
rs3213570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3213572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3897746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3901854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4454799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs471688	1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs4767935	0.85[CEU][hapmap]
rs4767937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];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]
rs508595	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs520753	0.91[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs525425	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs531782	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];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	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs624216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs625228	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs647881	0.84[ASN][1000 genomes]
rs661647	1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs909053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9431	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.80[ASN][1000 genomes]
rs989987	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs989986	HPD	cis	parietal	SCAN
rs989986	UNQ1887	Cis_1M	lymphoblastoid	RTeQTL
rs989986	ACADS	cis	Thyroid	GTEx
rs989986	SPPL3	cis	Nerve Tibial	GTEx
rs989986	SRRM4	cis	cerebellum	SCAN
rs989986	SPPL3	cis	Adipose Subcutaneous	GTEx
rs989986	SPPL3	cis	cerebellum	SCAN
rs989986	SPPL3	cis	parietal	SCAN
rs989986	WSB2	cis	cerebellum	SCAN

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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