Variant report

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

rs_ID	r²[population]
rs10494951	1.00[ASW][hapmap];0.85[LWK][hapmap];0.80[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap]
rs10779569	1.00[YRI][hapmap]
rs11119865	1.00[YRI][hapmap]
rs11119919	1.00[YRI][hapmap]
rs11576437	0.81[TSI][hapmap]
rs11580285	0.81[TSI][hapmap]
rs11589817	0.81[TSI][hapmap]
rs11590242	1.00[ASW][hapmap];0.84[TSI][hapmap]
rs12064553	0.84[EUR][1000 genomes]
rs12122247	1.00[YRI][hapmap]
rs12125159	1.00[YRI][hapmap]
rs12125796	1.00[YRI][hapmap]
rs12126761	1.00[YRI][hapmap]
rs12130548	1.00[YRI][hapmap]
rs12131060	1.00[YRI][hapmap]
rs12132233	1.00[YRI][hapmap]
rs12144884	1.00[YRI][hapmap]
rs12145020	1.00[YRI][hapmap]
rs12727947	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap]
rs12728266	0.81[TSI][hapmap]
rs12740519	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12746203	0.80[EUR][1000 genomes]
rs17719838	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2120770	0.81[TSI][hapmap]
rs2358448	1.00[YRI][hapmap]
rs2358454	1.00[YRI][hapmap]
rs34515259	0.82[EUR][1000 genomes]
rs34836421	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35556190	0.80[EUR][1000 genomes]
rs4540733	0.92[CEU][hapmap]
rs4951573	1.00[YRI][hapmap]
rs6661987	1.00[YRI][hapmap]
rs6676208	0.93[CEU][hapmap];0.87[TSI][hapmap]
rs6693849	0.93[CEU][hapmap]
rs71646142	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71646143	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71646153	0.89[EUR][1000 genomes]
rs7518399	1.00[ASW][hapmap]
rs7529198	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7546833	ATF3	cis	parietal	SCAN
rs7546833	RP11-15I11.3	cis	lung	GTEx
rs7546833	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx
rs7546833	SYT14	cis	cerebellum	SCAN
rs7546833	RPS4Y1	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212368800-212391000	Weak transcription	Thymus	Thymus
2	chr1:212375200-212379600	Enhancers	Placenta	Placenta
3	chr1:212376000-212382400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr1:212376200-212380000	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:212376200-212380600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:212376400-212380600	Weak transcription	Left Ventricle	heart
7	chr1:212376800-212382400	Weak transcription	HepG2	liver
8	chr1:212377600-212379800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:212378400-212379600	Weak transcription	Brain Anterior Caudate	brain
10	chr1:212378800-212380400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:212379000-212379800	Enhancers	K562	blood
12	chr1:212379200-212381600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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