Variant report

Variant	rs1361686
Chromosome Location	chr6:82707154-82707155
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	chr6:82460131..82462591-chr6:82705009..82708552,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112773	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10755418	0.83[EUR][1000 genomes]
rs10806231	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10806232	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10806233	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10806234	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10943838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10943841	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10943842	0.83[EUR][1000 genomes]
rs10943845	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12199470	0.89[EUR][1000 genomes]
rs12212514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12213171	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12215152	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12525526	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1342193	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1361688	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1418299	0.83[EUR][1000 genomes]
rs1418300	0.83[EUR][1000 genomes]
rs1418301	0.84[EUR][1000 genomes]
rs1857114	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1857115	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1935416	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2185729	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2323536	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2875088	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4262223	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4292569	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4637689	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4706148	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4706149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4706150	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4706914	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4706915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4706917	0.83[EUR][1000 genomes]
rs6903637	0.84[EUR][1000 genomes]
rs6937709	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6939071	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7754923	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7770981	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1361686	FAM46A	cis	cerebellum	SCAN
rs1361686	TBX18	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:82703600-82708000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:82704400-82708200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr6:82704400-82708200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:82704400-82708200	Enhancers	HSMM	muscle
5	chr6:82704400-82709400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:82704600-82707200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:82705000-82708400	Enhancers	NHLF	lung
8	chr6:82705000-82709600	Enhancers	NH-A	brain
9	chr6:82705400-82707800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:82705400-82708200	Enhancers	K562	blood
11	chr6:82705400-82710800	Enhancers	HMEC	breast
12	chr6:82705600-82707200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:82705800-82707200	Weak transcription	A549	lung
14	chr6:82705800-82708000	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr6:82705800-82709000	Weak transcription	HepG2	liver
16	chr6:82706000-82708000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:82706000-82708400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:82706000-82709200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:82706200-82715000	Weak transcription	Placenta	Placenta
20	chr6:82706400-82707200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:82706400-82707400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr6:82706400-82707800	Enhancers	Primary hematopoietic stem cells	blood
23	chr6:82706400-82707800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:82706400-82708000	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr6:82706400-82708200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr6:82706400-82708200	Enhancers	GM12878-XiMat	blood
27	chr6:82706400-82708200	Enhancers	HSMMtube	muscle
28	chr6:82706800-82707600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:82706800-82708000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:82706800-82709200	Enhancers	NHDF-Ad	bronchial
31	chr6:82707000-82707200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:82707000-82707400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:82707000-82707400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:82707000-82707400	Flanking Active TSS	NHEK	skin
35	chr6:82707000-82707600	Flanking Active TSS	Hela-S3	cervix
36	chr6:82707000-82708200	Flanking Active TSS	Osteobl	bone
37	chr6:82707000-82709400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:82707000-82710600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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