Variant report

Variant	rs1866242
Chromosome Location	chr2:86187595-86187596
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86178306..86181703-chr2:86184579..86188621,5	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10181091	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10181916	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10183118	0.84[EUR][1000 genomes]
rs10186005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189191	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198260	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1020095	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11890514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891625	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472588	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476390	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714161	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12714163	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714164	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12714165	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13000793	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13397189	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1438153	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1438155	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561330	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866243	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1866245	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4346389	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4480982	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4514874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832018	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4832020	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6547651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706720	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708525	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713002	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6728146	0.81[EUR][1000 genomes]
rs6737454	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6740044	0.81[CHD][hapmap]
rs7597264	0.87[ASN][1000 genomes]
rs934830	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[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	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1866242	PTCD3	cis	cerebellum	SCAN
rs1866242	MRPL35	cis	parietal	SCAN
rs1866242	C2orf51	cis	cerebellum	SCAN
rs1866242	IMMT	cis	cerebellum	SCAN
rs1866242	IMMT	cis	uninvolved skin	skin_eQTL
rs1866242	ST3GAL5	cis	cerebellum	SCAN
rs1866242	IMMT	Cis_1M	lymphoblastoid	RTeQTL
rs1866242	MRPL35	cis	cerebellum	SCAN
rs1866242	REEP1	cis	parietal	SCAN
rs1866242	IMMT	cis	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86178800-86188200	Enhancers	Fetal Muscle Leg	muscle
2	chr2:86180200-86187600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:86180800-86188600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:86182600-86187600	Weak transcription	Esophagus	oesophagus
5	chr2:86183600-86187600	Weak transcription	Pancreas	Pancrea
6	chr2:86183800-86190800	Weak transcription	Stomach Mucosa	stomach
7	chr2:86184400-86187600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:86184600-86188400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:86184800-86188200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:86186400-86188000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:86186600-86187800	Enhancers	Psoas Muscle	Psoas
12	chr2:86186600-86187800	Enhancers	HSMMtube	muscle
13	chr2:86186800-86187600	Weak transcription	Right Ventricle	heart
14	chr2:86187200-86187600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr2:86187200-86188000	Weak transcription	A549	lung
16	chr2:86187400-86189200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:86187400-86189200	Enhancers	Fetal Muscle Trunk	muscle

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