Variant report

Variant	rs7303677
Chromosome Location	chr12:48478539-48478540
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	chr12:48477561..48478652-chr12:48558658..48559651,7	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10492081	0.81[ASW][hapmap];0.81[CHB][hapmap];0.86[YRI][hapmap]
rs10492082	0.87[EUR][1000 genomes]
rs1049392	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747529	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10875733	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10875739	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10875741	0.86[ASN][1000 genomes]
rs10875744	0.84[ASN][1000 genomes]
rs10875752	0.93[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs10875754	1.00[JPT][hapmap]
rs10875761	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs10875766	1.00[JPT][hapmap]
rs11168350	0.94[JPT][hapmap]
rs11168353	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs11168354	1.00[JPT][hapmap]
rs11168358	1.00[JPT][hapmap]
rs11168363	0.81[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11168364	0.81[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11168373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168378	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11168412	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168417	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168419	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168424	0.87[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168434	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168435	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11168438	1.00[JPT][hapmap]
rs11168445	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11168448	0.90[CEU][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs11168453	0.90[CEU][hapmap];0.89[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs11168454	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11832455	0.87[ASN][1000 genomes]
rs11834818	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12228924	0.90[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12422355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12423250	0.94[JPT][hapmap]
rs12425679	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12426981	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17122567	0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1859443	0.94[JPT][hapmap]
rs1978161	1.00[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2107640	0.92[ASN][1000 genomes]
rs2158515	0.84[ASN][1000 genomes]
rs2240306	0.93[EUR][1000 genomes]
rs2286020	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2408954	1.00[JPT][hapmap]
rs3742075	1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3825403	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4258439	0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs56129148	0.90[ASN][1000 genomes]
rs57430775	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58540891	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58556309	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59667534	0.89[EUR][1000 genomes]
rs6580658	0.80[JPT][hapmap]
rs7138917	0.85[ASN][1000 genomes]
rs7299704	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7302354	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7304428	0.86[ASN][1000 genomes]
rs73104071	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7484942	0.83[CEU][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap]
rs765260	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7962390	0.90[CEU][hapmap];0.89[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs7962569	0.96[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap]
rs8181670	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap]
rs886589	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs954326	0.94[JPT][hapmap]
rs9651981	0.96[GIH][hapmap];0.94[JPT][hapmap]
rs9804751	0.96[GIH][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7303677	C12orf41	cis	parietal	SCAN
rs7303677	TMEM106C	cis	parietal	SCAN

Chromatin state (count:124 , 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	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
4	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:48454600-48478800	Weak transcription	Pancreas	Pancrea
8	chr12:48457400-48482000	Weak transcription	Right Ventricle	heart
9	chr12:48457600-48478600	Weak transcription	HSMMtube	muscle
10	chr12:48459200-48479000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:48464600-48489400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:48464800-48482400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:48465000-48478800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:48465000-48478800	Weak transcription	Aorta	Aorta
15	chr12:48465000-48487400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:48466200-48481400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:48466800-48478800	Weak transcription	Esophagus	oesophagus
18	chr12:48468200-48478800	Weak transcription	HepG2	liver
19	chr12:48468400-48478600	Weak transcription	Colonic Mucosa	Colon
20	chr12:48468400-48478800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr12:48468400-48481400	Weak transcription	NHDF-Ad	bronchial
22	chr12:48468400-48482200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr12:48468400-48482200	Weak transcription	Brain Substantia Nigra	brain
24	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:48468800-48478800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:48468800-48482800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr12:48470200-48497600	Weak transcription	Fetal Heart	heart
29	chr12:48470800-48492800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:48471400-48492000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:48472200-48489400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:48472400-48492000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr12:48472600-48486400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:48472600-48490200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:48472600-48490200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:48472600-48493600	Strong transcription	Fetal Thymus	thymus
37	chr12:48472800-48483200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:48472800-48493800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:48473000-48494800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:48473200-48478800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:48473200-48482600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr12:48473200-48486200	Strong transcription	Placenta	Placenta
43	chr12:48473200-48492000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:48473600-48490000	Strong transcription	Primary T cells from cord blood	blood
45	chr12:48473600-48495400	Strong transcription	Dnd41	blood
46	chr12:48473800-48480000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr12:48473800-48491600	Strong transcription	Duodenum Mucosa	Duodenum
48	chr12:48473800-48492800	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:48474000-48479600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:48474000-48484600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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