Variant report

Variant	rs1018973
Chromosome Location	chr12:48441692-48441693
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48409071..48411163-chr12:48439800..48441969,2	MCF-7	breast:
2	chr12:48399203..48401006-chr12:48440249..48442960,2	K562	blood:
3	chr12:48415871..48417650-chr12:48439843..48442703,2	MCF-7	breast:
4	chr12:48441127..48442750-chr12:48551016..48553176,2	K562	blood:
5	chr12:48417372..48419126-chr12:48439664..48441801,2	MCF-7	breast:
6	chr12:48440309..48443140-chr12:48444434..48446613,2	K562	blood:

Variant related genes	Relation type
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10492080	0.92[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10783226	0.83[EUR][1000 genomes]
rs10783227	0.88[EUR][1000 genomes]
rs10783231	0.83[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10783232	0.81[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs11168451	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11168455	0.81[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs11609399	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs11612578	0.94[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11612970	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11613485	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs11613781	0.83[EUR][1000 genomes]
rs12580764	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12581972	0.87[EUR][1000 genomes]
rs12822085	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1476608	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[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];0.89[EUR][1000 genomes]
rs1635526	0.81[EUR][1000 genomes]
rs17122565	0.89[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs17122611	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17122612	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[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];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17122613	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17122651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs1793931	0.83[EUR][1000 genomes]
rs1793933	0.83[EUR][1000 genomes]
rs1859441	0.83[ASW][hapmap];0.93[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.97[EUR][1000 genomes]
rs1859444	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs1968071	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[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];0.89[EUR][1000 genomes]
rs1990029	0.92[EUR][1000 genomes]
rs2286022	0.93[EUR][1000 genomes]
rs3742074	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[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];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3803183	0.88[EUR][1000 genomes]
rs3803184	0.88[EUR][1000 genomes]
rs3825404	0.81[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs4075913	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4141065	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs4293182	0.92[EUR][1000 genomes]
rs4589362	0.89[EUR][1000 genomes]
rs4760611	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760614	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760615	0.98[EUR][1000 genomes]
rs4760618	0.95[EUR][1000 genomes]
rs4760620	0.92[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap]
rs4760677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760683	0.81[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap]
rs4760685	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs4760692	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4760698	0.81[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs57054831	0.89[EUR][1000 genomes]
rs57380031	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57655233	0.81[EUR][1000 genomes]
rs58046797	0.89[EUR][1000 genomes]
rs58331734	0.83[EUR][1000 genomes]
rs59766465	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60567660	0.89[EUR][1000 genomes]
rs60629297	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60681522	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6580647	0.81[CEU][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes]
rs6580649	0.81[CEU][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs6580651	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580656	0.87[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap]
rs6580660	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7132668	0.91[EUR][1000 genomes]
rs7133249	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs726354	0.92[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs72644841	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72644842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72644843	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72644844	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72644845	0.83[EUR][1000 genomes]
rs72644847	0.81[EUR][1000 genomes]
rs7296913	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs7305954	0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs7310579	0.98[EUR][1000 genomes]
rs7312326	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs7315258	0.87[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap]
rs7485057	0.95[GIH][hapmap];1.00[JPT][hapmap]
rs757556	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs7957764	0.98[EUR][1000 genomes]
rs7959755	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs7967762	0.87[CEU][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs7969749	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7971668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs879242	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs9651993	0.92[EUR][1000 genomes]
rs9805048	0.92[TSI][hapmap];0.91[EUR][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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1018973	ZNF641	cis	Whole Blood	GTEx
rs1018973	ASB8	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48431800-48456600	Weak transcription	NHLF	lung
2	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:48435200-48445600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
6	chr12:48435400-48444600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:48435400-48457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:48435600-48444800	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:48435600-48445800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:48435800-48444600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:48435800-48445800	Strong transcription	Primary B cells from cord blood	blood
12	chr12:48435800-48452400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:48436000-48445000	Strong transcription	Fetal Muscle Leg	muscle
14	chr12:48436000-48445800	Strong transcription	Fetal Thymus	thymus
15	chr12:48436000-48448200	Strong transcription	Primary T cells from cord blood	blood
16	chr12:48436200-48444600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:48436200-48445800	Strong transcription	Dnd41	blood
18	chr12:48436400-48443400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:48436400-48443400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr12:48436400-48444000	Strong transcription	Fetal Lung	lung
21	chr12:48436400-48444200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:48436400-48444200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:48436400-48444200	Strong transcription	Brain Angular Gyrus	brain
24	chr12:48436400-48444600	Strong transcription	Placenta	Placenta
25	chr12:48436400-48444800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:48436400-48445200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:48436600-48444600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:48436600-48445800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:48436800-48441800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:48436800-48443000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:48436800-48443000	Strong transcription	NH-A	brain
32	chr12:48436800-48443800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:48436800-48444200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:48436800-48444600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr12:48437000-48443200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:48437000-48443400	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr12:48437000-48443800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:48437000-48444400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:48437000-48444400	Strong transcription	Liver	Liver
40	chr12:48437000-48444400	Strong transcription	GM12878-XiMat	blood
41	chr12:48437000-48444600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:48437000-48444600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr12:48437000-48445400	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:48437200-48443000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr12:48437400-48444200	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:48437400-48445200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr12:48437600-48443400	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr12:48437600-48444600	Strong transcription	Adipose Nuclei	Adipose
50	chr12:48437800-48444800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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