Variant report

Variant	rs1548022
Chromosome Location	chr7:26801250-26801251
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10224133	0.82[EUR][1000 genomes]
rs10227140	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10231161	0.81[CEU][hapmap]
rs10232697	0.82[EUR][1000 genomes]
rs10238253	0.81[EUR][1000 genomes]
rs10241952	0.81[EUR][1000 genomes]
rs1024454	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10245162	0.81[EUR][1000 genomes]
rs10247509	0.82[EUR][1000 genomes]
rs10255249	0.82[EUR][1000 genomes]
rs10256799	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10261915	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs10263118	0.81[EUR][1000 genomes]
rs10273468	0.82[EUR][1000 genomes]
rs10276636	0.82[EUR][1000 genomes]
rs1030644	0.82[EUR][1000 genomes]
rs10951145	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs10951149	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1123157	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1123158	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs11764558	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11770043	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs11770344	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11773029	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs11773050	0.82[EUR][1000 genomes]
rs12700754	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12700755	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs12700756	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12700757	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12700758	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs12700759	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs12700760	0.82[EUR][1000 genomes]
rs12700761	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12700762	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13186	0.84[CEU][hapmap]
rs1548478	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1548479	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1548480	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1859101	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2017794	0.82[EUR][1000 genomes]
rs2023819	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2023821	0.92[EUR][1000 genomes]
rs212842	0.85[CEU][hapmap]
rs212844	0.83[CEU][hapmap]
rs212845	0.94[EUR][1000 genomes]
rs212847	0.85[CEU][hapmap]
rs212851	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs212852	0.81[CEU][hapmap]
rs212853	0.82[CEU][hapmap]
rs212854	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs212858	0.81[CEU][hapmap]
rs2237328	0.82[CEU][hapmap]
rs2282906	0.85[CEU][hapmap]
rs2299101	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2299102	0.85[CEU][hapmap]
rs2391359	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2391360	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs28403911	0.81[EUR][1000 genomes]
rs3801839	0.82[AMR][1000 genomes]
rs3801853	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs3801854	0.80[EUR][1000 genomes]
rs3801855	0.81[EUR][1000 genomes]
rs3801860	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs3801864	0.82[EUR][1000 genomes]
rs3801872	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4345466	0.81[EUR][1000 genomes]
rs4512299	0.81[EUR][1000 genomes]
rs4573150	0.81[EUR][1000 genomes]
rs4719879	0.80[EUR][1000 genomes]
rs4722628	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4722631	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs4722632	0.90[ASN][1000 genomes]
rs4722634	0.81[EUR][1000 genomes]
rs4722637	0.99[ASN][1000 genomes]
rs484426	0.81[AMR][1000 genomes]
rs498561	0.81[AMR][1000 genomes]
rs5012512	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs58988613	0.80[EUR][1000 genomes]
rs6461961	0.82[CEU][hapmap]
rs6461964	0.80[CEU][hapmap]
rs6461965	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs6461971	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs648297	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs687254	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs687603	0.83[AMR][1000 genomes]
rs6943568	0.80[EUR][1000 genomes]
rs6970591	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs6973237	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs744611	0.81[EUR][1000 genomes]
rs744612	0.80[EUR][1000 genomes]
rs7777316	0.82[EUR][1000 genomes]
rs7784206	0.82[EUR][1000 genomes]
rs7784257	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7784548	0.82[EUR][1000 genomes]
rs7793663	0.80[EUR][1000 genomes]
rs7794399	0.81[EUR][1000 genomes]
rs7795313	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7802771	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7802852	0.80[EUR][1000 genomes]
rs7807640	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7810179	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs891874	0.81[EUR][1000 genomes]
rs891875	0.81[EUR][1000 genomes]
rs891876	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs934410	0.82[EUR][1000 genomes]
rs9648018	0.82[EUR][1000 genomes]
rs9648020	0.82[EUR][1000 genomes]
rs9648021	0.80[EUR][1000 genomes]
rs9648330	0.82[EUR][1000 genomes]
rs9648331	0.81[EUR][1000 genomes]
rs989250	0.83[CEU][hapmap];0.81[EUR][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	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1548022	SKAP2	cis	Whole Blood	GTEx
rs1548022	HOXA2	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26750400-26812000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:26779600-26810600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:26779800-26809000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr7:26781000-26809200	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr7:26796000-26808800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr7:26797800-26809400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr7:26797800-26812000	Weak transcription	Fetal Lung	lung
8	chr7:26798200-26809400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:26799000-26801400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr7:26799600-26809400	Weak transcription	Primary B cells from cord blood	blood
11	chr7:26799800-26812000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr7:26800800-26809400	Weak transcription	Primary hematopoietic stem cells	blood

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