Variant report

Variant	rs2472751
Chromosome Location	chr2:179539903-179539904
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	chr2:179537583..179540375-chr2:179542261..179543923,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLEKHA3-1	chr2:179539829-179540004	ENSG00000237298.4

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1001238	0.94[ASW][hapmap];0.84[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12693162	0.94[ASW][hapmap];0.82[CEU][hapmap];0.84[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1560221	0.94[ASW][hapmap];0.84[CEU][hapmap];0.89[GIH][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16866400	0.94[TSI][hapmap]
rs16866418	0.82[TSI][hapmap]
rs16866420	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2042995	0.94[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2042996	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2163009	0.94[ASW][hapmap];0.84[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2255167	0.86[ASN][1000 genomes]
rs2303828	0.85[TSI][hapmap]
rs2303838	0.82[TSI][hapmap]
rs2366751	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562830	0.82[TSI][hapmap]
rs2562834	0.82[TSI][hapmap]
rs2562838	0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs2562839	0.82[TSI][hapmap]
rs2562845	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[ASN][1000 genomes]
rs2562848	0.89[MKK][hapmap]
rs2627038	0.82[MKK][hapmap]
rs2627043	0.82[TSI][hapmap]
rs2742327	0.82[TSI][hapmap]
rs36113194	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3731750	1.00[ASW][hapmap];0.94[CEU][hapmap];0.87[GIH][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3769864	1.00[ASW][hapmap];0.84[CEU][hapmap];0.87[GIH][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3813250	1.00[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3820978	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3829746	0.94[ASW][hapmap];0.89[CEU][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4894029	1.00[ASW][hapmap];0.84[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6712785	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6735077	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs957875	0.94[CEU][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9808377	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.86[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	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv1813473	chr2:179515899-179540690	Genic enhancers Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2472751	SSFA2	cis	parietal	SCAN

Chromatin state (count:26 , 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	chr2:179501000-179541800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:179518000-179540200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:179528200-179601200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:179528400-179563200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:179529600-179600600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:179529800-179543800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:179530000-179544000	Weak transcription	Psoas Muscle	Psoas
10	chr2:179530600-179542200	Weak transcription	Primary B cells from cord blood	blood
11	chr2:179530800-179540200	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:179531000-179543600	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:179531400-179542200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:179532200-179540200	Weak transcription	Left Ventricle	heart
15	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:179533800-179541600	Weak transcription	Primary T cells from cord blood	blood
17	chr2:179534400-179556200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:179534400-179576200	Weak transcription	Fetal Intestine Large	intestine
19	chr2:179534800-179541800	Weak transcription	Right Ventricle	heart
20	chr2:179536400-179540200	Weak transcription	Fetal Heart	heart
21	chr2:179536400-179540200	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr2:179536600-179544000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:179537200-179541800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr2:179538000-179540000	Weak transcription	HSMMtube	muscle
25	chr2:179538000-179542400	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:179538400-179591800	Weak transcription	Fetal Thymus	thymus

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