Variant report

Variant	rs1484116
Chromosome Location	chr2:179618462-179618463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179609931..179612126-chr2:179618103..179619984,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10497520	0.94[ASW][hapmap];0.82[GIH][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs1484119	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17076	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2291313	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2562830	0.93[CEU][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs2562834	0.95[JPT][hapmap];0.87[TSI][hapmap]
rs2562836	0.86[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs2562838	0.88[ASW][hapmap];0.86[CEU][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2562839	0.86[CEU][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs2627043	0.93[CEU][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs2742327	0.88[ASW][hapmap];0.93[CEU][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2742331	0.86[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs4471922	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6750145	0.81[TSI][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	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1484116	PRKRA	cis	parietal	SCAN
rs1484116	NFE2L2	cis	cerebellum	SCAN
rs1484116	SSFA2	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179483200-179655400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:179493000-179620800	Weak transcription	HSMM	muscle
3	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:179577800-179640800	Weak transcription	Fetal Intestine Large	intestine
5	chr2:179588200-179622800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr2:179590800-179640400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr2:179598600-179622200	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:179600800-179621200	Weak transcription	Pancreas	Pancrea
9	chr2:179605400-179662400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:179610400-179621000	Strong transcription	HSMMtube	muscle
11	chr2:179610800-179671400	Weak transcription	Ovary	ovary
12	chr2:179613000-179623600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:179613400-179620000	Weak transcription	HMEC	breast
14	chr2:179614200-179626400	Strong transcription	Primary T cells from cord blood	blood
15	chr2:179614200-179645200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:179614400-179632400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:179614800-179626600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr2:179614800-179628800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr2:179615000-179619000	Weak transcription	Left Ventricle	heart
20	chr2:179615000-179620000	Weak transcription	Right Ventricle	heart
21	chr2:179615000-179621000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:179615200-179619400	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr2:179615400-179619000	Weak transcription	Fetal Muscle Leg	muscle
24	chr2:179616000-179620800	Weak transcription	Primary B cells from cord blood	blood
25	chr2:179617000-179621200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:179617200-179627800	Weak transcription	Psoas Muscle	Psoas
27	chr2:179617400-179618600	Weak transcription	Fetal Heart	heart
28	chr2:179617400-179619000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:179617400-179622600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:179618400-179620000	Strong transcription	Fetal Muscle Trunk	muscle

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