Variant report

Variant	rs3801839
Chromosome Location	chr7:26833021-26833022
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	chr7:26831909..26834634-chr7:26834764..26836802,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1024454	0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs11764558	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11770344	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs12700754	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs12700757	0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs12700762	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1548022	0.82[AMR][1000 genomes]
rs212851	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs212854	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs213527	0.92[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes]
rs2299101	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2769364	0.81[CEU][hapmap]
rs2769365	0.82[CEU][hapmap]
rs3801806	0.89[TSI][hapmap]
rs3801872	0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap]
rs4722628	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs484426	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs496173	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs498561	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs601106	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs607099	0.89[TSI][hapmap]
rs643036	0.94[EUR][1000 genomes]
rs648297	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs687603	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs757129	0.83[ASW][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7784257	0.81[AMR][1000 genomes]
rs7795313	0.92[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap]
rs7802771	1.00[CHB][hapmap];0.95[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3801839	HOXA6	cis	parietal	SCAN
rs3801839	HOXA2	cis	Whole Blood	GTEx
rs3801839	SKAP2	cis	Whole Blood	GTEx
rs3801839	HOTAIRM1	cis	Whole Blood	GTEx
rs3801839	SKAP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26808000-26854800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:26810600-26835200	Weak transcription	Spleen	Spleen
3	chr7:26812400-26849000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr7:26812800-26841600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:26813000-26834000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr7:26813000-26871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr7:26816600-26834000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr7:26821000-26843000	Weak transcription	Fetal Lung	lung
9	chr7:26822400-26834000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:26823000-26834600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:26823000-26846400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr7:26823400-26833800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr7:26823400-26839600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:26825600-26837400	Weak transcription	Lung	lung
16	chr7:26827600-26835200	Weak transcription	Primary B cells from cord blood	blood
17	chr7:26827600-26836800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:26831600-26833600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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