Variant report

Variant	rs278109
Chromosome Location	chr12:120171995-120171996
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120169454..120172109-chr12:120174649..120176647,2	MCF-7	breast:
2	chr12:120166136..120169033-chr12:120170815..120173425,2	K562	blood:
3	chr12:120169433..120172191-chr12:120174116..120175962,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10849691	0.80[ASN][1000 genomes]
rs11064884	0.80[ASN][1000 genomes]
rs12296121	0.82[ASN][1000 genomes]
rs1318272	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs175877	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs175879	0.82[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs202984	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs202985	0.85[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs203326	0.83[CHB][hapmap]
rs203327	0.94[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs203328	0.88[ASN][1000 genomes]
rs203329	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs203331	0.83[CHB][hapmap]
rs203332	0.82[CHD][hapmap]
rs2074052	0.83[CHB][hapmap];0.98[CHD][hapmap];0.81[ASN][1000 genomes]
rs2269939	0.82[ASW][hapmap]
rs2285595	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2393550	0.95[TSI][hapmap]
rs278103	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs278108	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.82[EUR][1000 genomes]
rs278111	0.89[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]
rs278115	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs278117	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278118	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs278128	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278129	0.83[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278130	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278131	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278132	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278133	0.80[CEU][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap]
rs278135	1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs278136	0.80[CEU][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap]
rs278137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs278139	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs278141	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs278142	0.89[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2936830	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2936831	0.90[ASN][1000 genomes]
rs2952403	0.85[ASN][1000 genomes]
rs2952444	0.83[CHB][hapmap];0.98[CHD][hapmap];0.84[ASN][1000 genomes]
rs2996027	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2996028	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2996029	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs2996030	0.90[ASN][1000 genomes]
rs3213625	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3213626	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs35070805	0.83[ASN][1000 genomes]
rs385930	0.82[CHD][hapmap]
rs402811	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs404447	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4766946	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4766947	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs4767839	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs7131914	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7132952	0.80[ASN][1000 genomes]
rs7299963	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7961569	0.87[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs904654	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs904655	0.82[CHD][hapmap];0.85[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs278109	UNC119B	cis	parietal	SCAN
rs278109	PRKAB1	cis	cerebellum	SCAN
rs278109	LRRC43	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120116800-120201800	Weak transcription	Fetal Heart	heart
2	chr12:120121200-120173400	Weak transcription	Primary B cells from cord blood	blood
3	chr12:120123400-120182000	Strong transcription	Dnd41	blood
4	chr12:120130800-120182200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:120143800-120211200	Weak transcription	Fetal Brain Male	brain
6	chr12:120149400-120224800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:120151600-120196600	Weak transcription	Gastric	stomach
8	chr12:120151800-120208400	Weak transcription	Fetal Brain Female	brain
9	chr12:120151800-120218600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:120154000-120177200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:120154800-120173400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:120154800-120174600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:120154800-120186000	Weak transcription	NH-A	brain
14	chr12:120154800-120209600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:120155000-120172800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:120156600-120174000	Weak transcription	Esophagus	oesophagus
17	chr12:120156600-120221400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:120156800-120173000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:120156800-120182600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:120158000-120173000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:120158000-120176800	Weak transcription	Spleen	Spleen
22	chr12:120158000-120186200	Weak transcription	Brain Germinal Matrix	brain
23	chr12:120158000-120186400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:120158200-120172000	Weak transcription	Brain Angular Gyrus	brain
25	chr12:120162800-120174400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:120163600-120186400	Weak transcription	HUVEC	blood vessel
27	chr12:120163800-120180000	Weak transcription	Brain Substantia Nigra	brain
28	chr12:120167400-120173600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:120167400-120176800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:120167600-120173400	Strong transcription	Thymus	Thymus
31	chr12:120168600-120181600	Weak transcription	GM12878-XiMat	blood
32	chr12:120169800-120173600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:120169800-120173600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:120169800-120173600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:120169800-120174400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:120170000-120173400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr12:120170000-120173400	Strong transcription	HMEC	breast
38	chr12:120170000-120173600	Strong transcription	Hela-S3	cervix
39	chr12:120170000-120173600	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr12:120170000-120173800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:120170000-120173800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:120170000-120174600	Strong transcription	NHDF-Ad	bronchial
43	chr12:120170200-120172600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:120170200-120173400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:120170200-120173600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr12:120170200-120174400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:120170400-120172400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr12:120170400-120172400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:120170400-120172400	Strong transcription	A549	lung
50	chr12:120170400-120173200	Strong transcription	Brain Cingulate Gyrus	brain

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