Variant report

Variant	rs7297303
Chromosome Location	chr12:117501788-117501789
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	chr12:117501550..117503831-chr12:117535985..117538295,2	MCF-7	breast:
2	chr12:117501229..117502760-chr12:117508705..117510581,2	K562	blood:

Variant related genes	Relation type
ENSG00000088992	Chromatin interaction
ENSG00000258285	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10735100	0.88[JPT][hapmap]
rs10735101	0.88[JPT][hapmap]
rs10744887	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774895	0.94[JPT][hapmap]
rs10774898	0.88[JPT][hapmap]
rs10774899	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10850734	0.88[JPT][hapmap]
rs10850745	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10850746	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10850747	0.84[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10850751	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10850752	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068299	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11068300	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068301	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11068306	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11611741	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11832441	0.84[EUR][1000 genomes]
rs11834817	0.95[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11837022	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12368876	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1472523	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2062528	0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2173654	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2291911	0.89[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2291916	0.88[JPT][hapmap];0.84[MEX][hapmap]
rs2393124	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3782191	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782192	0.86[EUR][1000 genomes]
rs4766816	0.88[JPT][hapmap]
rs4766823	0.88[JPT][hapmap]
rs4766825	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4767477	0.88[JPT][hapmap]
rs55969361	0.84[EUR][1000 genomes]
rs58470318	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59756806	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6490103	0.88[JPT][hapmap]
rs6490104	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6490105	0.82[CEU][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6490106	0.88[CEU][hapmap];0.81[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6490107	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7133090	0.88[JPT][hapmap]
rs7294692	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7297917	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7486428	0.88[JPT][hapmap]
rs7953553	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956481	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7960638	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7960731	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7964668	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7964686	0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs7968761	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7968891	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971795	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972416	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7978810	0.84[EUR][1000 genomes]
rs9634171	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7297303	C12orf49	cis	parietal	SCAN
rs7297303	TESC	cis	parietal	SCAN
rs7297303	BRAP	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117494800-117509800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr12:117495400-117502600	Weak transcription	A549	lung
3	chr12:117497800-117506000	Enhancers	Primary hematopoietic stem cells	blood
4	chr12:117498600-117502000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:117498800-117514600	Strong transcription	HepG2	liver
6	chr12:117499000-117522000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:117499200-117502200	Weak transcription	Brain Substantia Nigra	brain
8	chr12:117499200-117507600	Weak transcription	Right Atrium	heart
9	chr12:117499200-117507800	Weak transcription	Lung	lung
10	chr12:117499600-117506800	Weak transcription	K562	blood
11	chr12:117499600-117512400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:117500200-117501800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:117500400-117502000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr12:117500400-117502200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:117500400-117502400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr12:117500400-117502400	Enhancers	Placenta	Placenta
17	chr12:117500400-117502800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr12:117500600-117501800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:117500600-117502000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr12:117500600-117502200	Enhancers	Adipose Nuclei	Adipose
21	chr12:117500600-117503800	Weak transcription	Left Ventricle	heart
22	chr12:117500800-117502000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr12:117500800-117502400	Enhancers	Fetal Heart	heart
24	chr12:117501000-117501800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr12:117501000-117505000	Weak transcription	Brain Anterior Caudate	brain
26	chr12:117501000-117507400	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:117501200-117501800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:117501200-117502200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:117501200-117503400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:117501200-117510000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:117501400-117501800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr12:117501400-117501800	Weak transcription	Stomach Mucosa	stomach
33	chr12:117501400-117502000	Enhancers	Thymus	Thymus
34	chr12:117501400-117502200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:117501400-117502400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr12:117501400-117502600	Enhancers	Primary B cells from cord blood	blood
37	chr12:117501400-117503000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr12:117501400-117503000	Enhancers	GM12878-XiMat	blood
39	chr12:117501400-117503600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:117501400-117518600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:117501600-117501800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:117501600-117501800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
43	chr12:117501600-117502200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:117501600-117502400	Enhancers	Primary T cells from cord blood	blood
45	chr12:117501600-117502400	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr12:117501600-117502400	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr12:117501600-117502400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr12:117501600-117502600	Weak transcription	Pancreas	Pancrea
49	chr12:117501600-117502800	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:117501600-117503400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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