Variant report

Variant	rs11613485
Chromosome Location	chr12:48462455-48462456
allele	C/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	POLR2A	chr12:48462341-48462472	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48459890..48462494-chr12:48464118..48467480,3	K562	blood:
2	chr12:48460907..48463410-chr12:48550372..48552921,3	K562	blood:

Variant related genes	Relation type
SENP1	TF binding region
ENSG00000177981	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[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];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10783227	0.80[EUR][1000 genomes]
rs10783231	0.83[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs10783232	0.80[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs10875742	0.84[ASN][1000 genomes]
rs11168451	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11168455	0.80[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs11609399	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11612578	0.94[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs11612970	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11613781	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12580764	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12581972	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822085	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs1476608	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]
rs17122565	0.91[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap]
rs17122611	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17122613	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1859441	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.89[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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1990029	0.85[EUR][1000 genomes]
rs2286022	0.85[EUR][1000 genomes]
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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803183	0.80[EUR][1000 genomes]
rs3803184	0.80[EUR][1000 genomes]
rs3825404	0.81[CEU][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs4075913	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4141065	0.93[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4293182	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4589362	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[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];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs4760614	0.92[EUR][1000 genomes]
rs4760615	0.90[EUR][1000 genomes]
rs4760618	0.88[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];0.91[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap]
rs4760677	0.92[EUR][1000 genomes]
rs4760683	0.81[CEU][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes]
rs4760685	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs4760692	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4760698	0.80[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs57054831	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57380031	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57655233	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58046797	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58331734	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59766465	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60567660	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60629297	0.86[EUR][1000 genomes]
rs60681522	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580647	0.81[CEU][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs6580649	0.81[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs6580651	0.92[EUR][1000 genomes]
rs6580656	0.86[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap]
rs6580660	0.80[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7132668	0.83[EUR][1000 genomes]
rs7133249	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72644841	0.89[EUR][1000 genomes]
rs72644842	0.92[EUR][1000 genomes]
rs72644843	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72644844	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72644845	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72644846	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs72644847	0.85[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];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7305954	0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs7310579	0.90[EUR][1000 genomes]
rs7312326	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[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];0.91[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap]
rs7485057	0.82[CHD][hapmap];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];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7957764	0.90[EUR][1000 genomes]
rs7959755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs7963934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967762	0.87[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs7969749	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7971668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs879242	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9651993	0.85[EUR][1000 genomes]
rs9805048	0.92[TSI][hapmap];0.84[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
rs11613485	ASB8	cis	parietal	SCAN
rs11613485	ZNF641	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
4	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
7	chr12:48441600-48468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:48444200-48474600	Weak transcription	Gastric	stomach
10	chr12:48444800-48468000	Weak transcription	Spleen	Spleen
11	chr12:48449400-48464400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:48452000-48468600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:48452000-48468800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:48452000-48468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:48452000-48469400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:48452200-48468600	Strong transcription	NH-A	brain
17	chr12:48452200-48468800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:48452200-48469000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr12:48452200-48469600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:48452200-48470000	Strong transcription	Placenta	Placenta
21	chr12:48452400-48463200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:48452400-48468800	Strong transcription	Adipose Nuclei	Adipose
23	chr12:48452400-48468800	Strong transcription	Duodenum Mucosa	Duodenum
24	chr12:48452400-48468800	Strong transcription	Fetal Thymus	thymus
25	chr12:48452400-48469600	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:48452600-48468400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:48452800-48468000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:48452800-48468600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:48453000-48464800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:48453000-48468400	Strong transcription	Fetal Lung	lung
31	chr12:48453000-48468800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr12:48453000-48469200	Weak transcription	Fetal Heart	heart
33	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr12:48453200-48469200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:48453600-48469800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr12:48453600-48471200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:48453800-48466000	Weak transcription	Esophagus	oesophagus
38	chr12:48453800-48469000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:48453800-48469000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr12:48453800-48469000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:48453800-48469000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:48453800-48469400	Strong transcription	A549	lung
43	chr12:48453800-48474800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:48454000-48469000	Strong transcription	Liver	Liver
45	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:48454600-48469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:48454600-48478800	Weak transcription	Pancreas	Pancrea
48	chr12:48454800-48472000	Strong transcription	Dnd41	blood
49	chr12:48455600-48463200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:48455600-48464400	Weak transcription	Lung	lung

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