Variant report

Variant	rs498561
Chromosome Location	chr7:26857494-26857495
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:26856308..26858205-chr7:26890312..26892173,2	K562	blood:
2	chr7:26855021..26857994-chr7:26859828..26861687,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1024454	0.84[JPT][hapmap]
rs11764558	0.84[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs11770344	0.84[JPT][hapmap]
rs12700754	0.84[JPT][hapmap]
rs12700756	0.81[AMR][1000 genomes]
rs12700757	0.84[JPT][hapmap]
rs12700762	0.84[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs1548022	0.81[AMR][1000 genomes]
rs212851	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs212854	0.83[JPT][hapmap]
rs213527	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2299101	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs2769364	0.87[CEU][hapmap]
rs3801806	0.83[CEU][hapmap]
rs3801839	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3801872	0.83[JPT][hapmap]
rs471536	0.81[EUR][1000 genomes]
rs4722628	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs475238	0.81[EUR][1000 genomes]
rs476098	0.81[EUR][1000 genomes]
rs484426	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496173	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs503110	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs504955	0.81[EUR][1000 genomes]
rs532320	0.81[EUR][1000 genomes]
rs556402	0.81[EUR][1000 genomes]
rs564260	0.81[EUR][1000 genomes]
rs57027817	0.81[EUR][1000 genomes]
rs570840	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs601106	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs607099	0.83[CEU][hapmap]
rs622011	0.81[EUR][1000 genomes]
rs639221	0.81[EUR][1000 genomes]
rs640512	0.81[EUR][1000 genomes]
rs643036	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs648297	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs667841	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs687254	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs687603	0.94[CHB][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs688039	0.81[EUR][1000 genomes]
rs757129	0.83[JPT][hapmap]
rs774367	0.82[EUR][1000 genomes]
rs7784257	0.82[AMR][1000 genomes]
rs7795313	0.83[JPT][hapmap]
rs7802771	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs7810179	0.84[AMR][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	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
3	nsv887855	chr7:26823963-26872652	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs498561	HOXA2	cis	Whole Blood	GTEx
rs498561	HOTAIRM1	cis	Whole Blood	GTEx
rs498561	SKAP2	cis	Whole Blood	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26813000-26871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:26839400-26871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:26843600-26870800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr7:26843600-26871400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:26843800-26863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr7:26850000-26869200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:26850200-26861800	Weak transcription	Primary B cells from cord blood	blood
9	chr7:26850200-26862600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr7:26850400-26862600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr7:26850400-26863400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr7:26850400-26871400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:26852600-26870600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:26853400-26882600	Weak transcription	Adipose Nuclei	Adipose
15	chr7:26853600-26872000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:26853800-26871400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:26854200-26876400	Weak transcription	Fetal Lung	lung
18	chr7:26856400-26871800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:26856600-26871400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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