Variant report

Variant	rs1476608
Chromosome Location	chr12:48493731-48493732
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48485766..48487842-chr12:48492763..48495149,2	MCF-7	breast:
2	chr12:48492914..48496557-chr12:48498180..48501677,4	MCF-7	breast:
3	chr12:48493205..48495553-chr12:48549427..48551502,2	MCF-7	breast:
4	chr12:48492802..48495479-chr12:48497432..48499214,2	K562	blood:

Variant related genes	Relation type
ENSG00000177981	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1018973	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]
rs10492080	0.92[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.91[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];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10783231	0.83[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10783232	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs10875742	0.90[ASN][1000 genomes]
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];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11612578	0.94[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs11612970	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11613485	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11613781	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12580764	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12581972	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822085	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1489111	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs17122565	0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap]
rs17122611	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17122612	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17122613	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17122651	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1859441	0.83[ASW][hapmap];0.93[CEU][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs1859444	0.81[CEU][hapmap]
rs1968071	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1990029	0.81[EUR][1000 genomes]
rs2258342	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs2286022	0.84[EUR][1000 genomes]
rs2634699	0.80[JPT][hapmap]
rs2732455	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs2732487	0.87[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs3742074	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];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825404	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs4075913	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4141065	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4293182	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4589362	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760611	0.93[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4760614	0.89[EUR][1000 genomes]
rs4760615	0.87[EUR][1000 genomes]
rs4760618	0.84[EUR][1000 genomes]
rs4760620	0.92[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[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];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs4760677	0.89[EUR][1000 genomes]
rs4760683	0.81[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4760685	0.89[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57380031	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57655233	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58046797	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58331734	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59766465	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60567660	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60629297	0.84[EUR][1000 genomes]
rs60681522	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6580647	0.81[CEU][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs6580649	0.81[CEU][hapmap];0.92[TSI][hapmap]
rs6580651	0.89[EUR][1000 genomes]
rs6580656	0.87[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs6580660	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7133249	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs726354	0.92[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.91[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];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72644841	0.85[EUR][1000 genomes]
rs72644842	0.89[EUR][1000 genomes]
rs72644843	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72644844	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72644845	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72644846	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72644847	0.92[EUR][1000 genomes]
rs7296913	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[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305954	0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs7310579	0.87[EUR][1000 genomes]
rs7312326	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315258	0.87[CEU][hapmap];0.83[CHB][hapmap];0.86[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];0.84[EUR][1000 genomes]
rs7485057	0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs7485824	0.86[EUR][1000 genomes]
rs757556	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7957764	0.87[EUR][1000 genomes]
rs7959755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs7963934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967762	0.87[CEU][hapmap];0.80[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs7969749	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7971668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs879242	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs901964	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs9651993	0.81[EUR][1000 genomes]
rs9805048	0.92[TSI][hapmap];0.81[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	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
2	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
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1476608	ASB8	cis	parietal	SCAN
rs1476608	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:48470200-48497600	Weak transcription	Fetal Heart	heart
7	chr12:48472800-48493800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:48473000-48494800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:48473600-48495400	Strong transcription	Dnd41	blood
10	chr12:48474000-48494800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:48475000-48498200	Weak transcription	Psoas Muscle	Psoas
12	chr12:48476800-48498400	Weak transcription	Fetal Brain Male	brain
13	chr12:48477200-48498200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr12:48477400-48498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:48479400-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr12:48479400-48498200	Weak transcription	Brain Angular Gyrus	brain
17	chr12:48479400-48498400	Weak transcription	Aorta	Aorta
18	chr12:48479600-48498000	Weak transcription	NHEK	skin
19	chr12:48480400-48498200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:48481200-48493800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr12:48482800-48498200	Weak transcription	NHDF-Ad	bronchial
22	chr12:48483000-48498200	Weak transcription	NH-A	brain
23	chr12:48483000-48498400	Weak transcription	HSMMtube	muscle
24	chr12:48483200-48498200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr12:48483200-48498200	Weak transcription	HepG2	liver
26	chr12:48483200-48498400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:48483200-48499200	Weak transcription	Small Intestine	intestine
28	chr12:48483400-48498200	Weak transcription	NHLF	lung
29	chr12:48484800-48498200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:48485000-48498200	Weak transcription	Spleen	Spleen
31	chr12:48486200-48499000	Weak transcription	Gastric	stomach
32	chr12:48486400-48497800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:48487200-48494400	Strong transcription	Fetal Stomach	stomach
34	chr12:48488000-48496800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:48488000-48498200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:48488200-48495400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:48488200-48497600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:48488200-48498200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:48488200-48498200	Weak transcription	Lung	lung
40	chr12:48488200-48498200	Weak transcription	Pancreas	Pancrea
41	chr12:48488200-48498400	Weak transcription	Brain Substantia Nigra	brain
42	chr12:48488200-48499200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:48488400-48494800	Strong transcription	Hela-S3	cervix
44	chr12:48488400-48498200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:48488400-48498400	Weak transcription	Right Ventricle	heart
46	chr12:48489000-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:48489600-48497200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:48489600-48498400	Weak transcription	Left Ventricle	heart
49	chr12:48489600-48499000	Weak transcription	Esophagus	oesophagus
50	chr12:48489800-48494000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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