Variant report

Variant	rs531782
Chromosome Location	chr12:121273247-121273248
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Variant related genes	Relation type
ENSG00000122971	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1027556	0.93[YRI][hapmap]
rs1039302	0.93[YRI][hapmap]
rs10431387	0.93[YRI][hapmap]
rs10437838	0.93[YRI][hapmap]
rs10774568	0.89[YRI][hapmap]
rs10774569	0.93[YRI][hapmap]
rs10774571	0.93[YRI][hapmap]
rs10774572	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10849786	0.88[YRI][hapmap]
rs10849788	0.85[YRI][hapmap]
rs10849791	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10849807	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10849810	0.93[YRI][hapmap]
rs10849811	0.93[YRI][hapmap]
rs11065259	0.93[YRI][hapmap]
rs11065264	0.81[ASN][1000 genomes]
rs11065282	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065283	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065284	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065292	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065293	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065298	0.93[YRI][hapmap]
rs11065300	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11065307	0.83[ASN][1000 genomes]
rs11065311	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs11065322	0.81[LWK][hapmap];0.93[YRI][hapmap]
rs11065324	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs1151849	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151859	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1151862	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11608262	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11611087	0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1168944	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168946	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168948	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1168953	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1177585	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1179939	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12371178	0.83[ASN][1000 genomes]
rs12580949	0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs12809299	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822123	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12825746	0.98[ASN][1000 genomes]
rs12831094	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13746	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1542859	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs1696357	0.87[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs1718180	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2015462	0.81[ASN][1000 genomes]
rs2047568	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2393717	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2393718	0.92[YRI][hapmap]
rs2461475	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2650017	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2893876	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3213566	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3213567	0.81[ASN][1000 genomes]
rs3213568	0.93[YRI][hapmap]
rs3213570	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3213571	0.93[YRI][hapmap]
rs3213572	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs34009825	0.83[ASN][1000 genomes]
rs34076777	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35706672	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35905305	0.82[ASN][1000 genomes]
rs3809313	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809314	0.93[YRI][hapmap]
rs3842985	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3861797	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3883901	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];0.95[ASN][1000 genomes]
rs3897746	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs3901854	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs4454799	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs471688	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766979	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766980	0.84[ASN][1000 genomes]
rs4767937	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs487943	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508595	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs520753	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs533264	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs548452	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs572016	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580240	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58291418	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58918988	0.82[ASN][1000 genomes]
rs590625	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602984	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs608394	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs609700	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs610694	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs618482	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs624216	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625228	0.83[ASW][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs647881	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6489780	0.81[LWK][hapmap];0.93[YRI][hapmap]
rs6489782	0.89[YRI][hapmap]
rs661647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665585	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs666976	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs668622	0.80[ASN][1000 genomes]
rs7135147	0.93[YRI][hapmap]
rs7137504	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs7139145	0.93[YRI][hapmap]
rs715319	0.81[LWK][hapmap];0.93[YRI][hapmap]
rs7298639	0.93[YRI][hapmap]
rs73413868	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7965332	0.93[YRI][hapmap]
rs7969140	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs869781	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs909053	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9431	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs989986	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]
rs989987	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs531782	RPLP0	cis	Skin Sun Exposed Lower leg	GTEx
rs531782	SPPL3	cis	cerebellum	SCAN
rs531782	SRRM4	cis	cerebellum	SCAN
rs531782	UNQ1887	cis	Temporal Cortex	GTEx
rs531782	WSB2	cis	cerebellum	SCAN
rs531782	P2RX4	cis	cerebellum	SCAN
rs531782	HPD	cis	parietal	SCAN
rs531782	SPPL3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121222200-121274000	Weak transcription	Lung	lung
2	chr12:121261600-121274400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:121264800-121275000	Enhancers	Brain Hippocampus Middle	brain
4	chr12:121265400-121273800	Enhancers	Brain Substantia Nigra	brain
5	chr12:121265400-121274200	Enhancers	Brain Angular Gyrus	brain
6	chr12:121266000-121274200	Enhancers	Brain Cingulate Gyrus	brain
7	chr12:121266400-121274600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:121266600-121274000	Enhancers	Brain Anterior Caudate	brain
9	chr12:121266800-121276200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:121267200-121282800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:121267600-121274000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr12:121267600-121285800	Weak transcription	Colonic Mucosa	Colon
13	chr12:121267800-121274800	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr12:121268400-121273800	Weak transcription	HSMM	muscle
15	chr12:121268400-121274000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:121268400-121274800	Enhancers	Rectal Smooth Muscle	rectum
17	chr12:121268600-121274200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:121268600-121274600	Enhancers	Adipose Nuclei	Adipose
19	chr12:121268600-121274600	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr12:121268600-121274800	Enhancers	Colon Smooth Muscle	Colon
21	chr12:121268600-121276200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:121268600-121276600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr12:121269000-121273600	Weak transcription	Esophagus	oesophagus
24	chr12:121269000-121273800	Weak transcription	Gastric	stomach
25	chr12:121269000-121278400	Weak transcription	Ovary	ovary
26	chr12:121269200-121274200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:121269600-121274000	Weak transcription	Stomach Mucosa	stomach
28	chr12:121269600-121274200	Weak transcription	Liver	Liver
29	chr12:121269800-121273400	Weak transcription	Fetal Stomach	stomach
30	chr12:121269800-121274000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:121269800-121274000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:121269800-121281200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:121269800-121281200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:121269800-121282800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr12:121269800-121291400	Weak transcription	Fetal Intestine Large	intestine
36	chr12:121270200-121274800	Enhancers	Fetal Thymus	thymus
37	chr12:121270200-121274800	Enhancers	Thymus	Thymus
38	chr12:121270400-121274400	Enhancers	Primary B cells from cord blood	blood
39	chr12:121270600-121273800	Flanking Active TSS	GM12878-XiMat	blood
40	chr12:121270600-121275200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr12:121270800-121273800	Enhancers	Primary T cells from cord blood	blood
42	chr12:121270800-121274000	Enhancers	NHDF-Ad	bronchial
43	chr12:121270800-121274200	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:121270800-121274800	Enhancers	Primary B cells from peripheral blood	blood
45	chr12:121271000-121274200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:121271000-121274400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:121271000-121274400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:121271000-121274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr12:121271000-121275000	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr12:121271200-121273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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