Variant report

Variant	rs3801835
Chromosome Location	chr7:26852053-26852054
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 178 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:175)

rs_ID	r²[population]
rs10085562	1.00[JPT][hapmap]
rs10085721	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10215738	0.81[AFR][1000 genomes]
rs10225924	0.83[AFR][1000 genomes]
rs10231080	1.00[JPT][hapmap]
rs10235680	1.00[JPT][hapmap]
rs10237921	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10239608	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10244986	0.87[AFR][1000 genomes]
rs10245367	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10246300	1.00[JPT][hapmap]
rs10246483	1.00[JPT][hapmap]
rs10246578	1.00[JPT][hapmap]
rs10246641	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10248232	1.00[JPT][hapmap]
rs10248500	0.83[AFR][1000 genomes]
rs10249383	1.00[JPT][hapmap]
rs10249824	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10250097	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10250223	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10250304	1.00[JPT][hapmap]
rs10251817	1.00[JPT][hapmap]
rs10252268	1.00[JPT][hapmap]
rs10254460	1.00[JPT][hapmap]
rs10254467	1.00[JPT][hapmap]
rs10256561	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10257057	1.00[JPT][hapmap]
rs10261927	1.00[JPT][hapmap]
rs10262212	1.00[JPT][hapmap]
rs10262414	0.86[AFR][1000 genomes]
rs10262527	1.00[JPT][hapmap]
rs10262797	1.00[JPT][hapmap]
rs10265607	1.00[JPT][hapmap]
rs10267950	0.83[AFR][1000 genomes]
rs10269731	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10271306	1.00[JPT][hapmap]
rs10271393	1.00[JPT][hapmap]
rs10272301	0.81[AFR][1000 genomes]
rs10272303	0.83[AFR][1000 genomes]
rs10275896	0.84[AFR][1000 genomes]
rs10277060	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1030647	1.00[JPT][hapmap]
rs10486473	1.00[JPT][hapmap]
rs10486474	1.00[JPT][hapmap]
rs10486480	1.00[JPT][hapmap]
rs10486481	1.00[JPT][hapmap]
rs11772673	0.83[EUR][1000 genomes]
rs12333525	0.81[AFR][1000 genomes]
rs12334154	1.00[JPT][hapmap]
rs12532199	0.88[AFR][1000 genomes]
rs12532339	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12532395	0.83[AFR][1000 genomes]
rs12535078	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12536560	0.84[AFR][1000 genomes]
rs12537323	0.86[AFR][1000 genomes]
rs12540045	0.83[AFR][1000 genomes]
rs13234201	0.83[EUR][1000 genomes]
rs13234336	0.83[EUR][1000 genomes]
rs13438513	0.86[AFR][1000 genomes]
rs13438514	0.83[AFR][1000 genomes]
rs17154428	1.00[JPT][hapmap]
rs17154538	1.00[JPT][hapmap]
rs17310268	1.00[JPT][hapmap]
rs17310851	1.00[JPT][hapmap]
rs17313134	1.00[JPT][hapmap]
rs17315334	0.87[AFR][1000 genomes]
rs17315775	0.86[AFR][1000 genomes]
rs17315929	0.83[AFR][1000 genomes]
rs17323962	1.00[JPT][hapmap]
rs17370293	1.00[JPT][hapmap]
rs17371905	1.00[JPT][hapmap]
rs2015543	0.83[EUR][1000 genomes]
rs2769364	0.90[ASN][1000 genomes]
rs2769365	0.90[ASN][1000 genomes]
rs28404962	0.84[AFR][1000 genomes]
rs28617235	0.84[AFR][1000 genomes]
rs28806787	0.83[AFR][1000 genomes]
rs34833677	0.85[ASN][1000 genomes]
rs3735547	1.00[JPT][hapmap]
rs3801806	0.82[ASN][1000 genomes]
rs3801820	0.86[AFR][1000 genomes]
rs3801821	0.86[AFR][1000 genomes]
rs3801822	0.86[AFR][1000 genomes]
rs3801825	0.86[AFR][1000 genomes]
rs3801826	0.86[AFR][1000 genomes]
rs3801827	0.86[AFR][1000 genomes]
rs3801828	0.86[AFR][1000 genomes]
rs3801829	0.88[AFR][1000 genomes]
rs3801830	0.87[AFR][1000 genomes]
rs3801831	0.88[AFR][1000 genomes]
rs3801832	0.88[AFR][1000 genomes]
rs3801833	0.88[AFR][1000 genomes]
rs3801834	0.88[AFR][1000 genomes]
rs3801837	0.88[AFR][1000 genomes]
rs3801840	0.81[AFR][1000 genomes]
rs3801847	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3801848	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3801850	0.83[AFR][1000 genomes]
rs3823930	0.86[AFR][1000 genomes]
rs3823931	0.88[AFR][1000 genomes]
rs3823932	0.88[AFR][1000 genomes]
rs3823933	0.88[AFR][1000 genomes]
rs3823936	0.88[AFR][1000 genomes]
rs3823938	0.88[AFR][1000 genomes]
rs3823939	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4141345	1.00[JPT][hapmap]
rs4141346	1.00[JPT][hapmap]
rs471536	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs4722633	0.82[EUR][1000 genomes]
rs4722644	0.81[AFR][1000 genomes]
rs475238	0.90[ASN][1000 genomes]
rs476098	0.90[ASN][1000 genomes]
rs490366	0.82[CHB][hapmap]
rs503110	0.91[ASN][1000 genomes]
rs504955	0.90[ASN][1000 genomes]
rs532320	0.90[ASN][1000 genomes]
rs534981	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs550141	0.82[CHB][hapmap]
rs556402	0.90[ASN][1000 genomes]
rs55739485	0.86[AFR][1000 genomes]
rs55836768	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55904994	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56359409	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs564260	0.90[ASN][1000 genomes]
rs567124	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs57027817	0.90[ASN][1000 genomes]
rs570840	0.86[ASN][1000 genomes]
rs57135974	0.88[AFR][1000 genomes]
rs580904	0.84[ASN][1000 genomes]
rs58760954	0.88[AFR][1000 genomes]
rs607099	0.90[ASN][1000 genomes]
rs622011	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs636371	0.82[CHB][hapmap]
rs639221	0.90[ASN][1000 genomes]
rs640512	0.90[ASN][1000 genomes]
rs6461973	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6461974	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6461975	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6461976	0.94[EUR][1000 genomes]
rs667841	0.91[ASN][1000 genomes]
rs688039	0.90[ASN][1000 genomes]
rs6944529	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6948584	0.83[AFR][1000 genomes]
rs6948657	0.86[AFR][1000 genomes]
rs6950668	1.00[JPT][hapmap]
rs6954621	1.00[JPT][hapmap]
rs6965167	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73065526	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73067435	0.88[AFR][1000 genomes]
rs73067443	0.88[AFR][1000 genomes]
rs73067456	0.87[AFR][1000 genomes]
rs73067475	0.86[AFR][1000 genomes]
rs73067476	0.86[AFR][1000 genomes]
rs73067479	0.83[AFR][1000 genomes]
rs774367	0.91[ASN][1000 genomes]
rs7779604	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7779843	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7782851	1.00[JPT][hapmap]
rs7783807	1.00[JPT][hapmap]
rs7784380	1.00[JPT][hapmap]
rs7785689	0.88[AFR][1000 genomes]
rs7785711	0.83[AFR][1000 genomes]
rs7785798	0.86[AFR][1000 genomes]
rs7785815	0.86[AFR][1000 genomes]
rs7785832	0.87[AFR][1000 genomes]
rs7785918	0.84[AFR][1000 genomes]
rs7786308	1.00[JPT][hapmap]
rs7786456	1.00[JPT][hapmap]
rs7798696	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7799888	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7802514	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7802715	0.84[AFR][1000 genomes]
rs7806174	1.00[JPT][hapmap]
rs7810109	0.83[EUR][1000 genomes]
rs7810127	0.83[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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3801835	SKAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:20 , 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	chr7:26813000-26871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:26839400-26871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:26843600-26870800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr7:26843600-26871400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:26843800-26863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:26844400-26853200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr7:26847200-26853000	Weak transcription	Ovary	ovary
10	chr7:26847400-26853200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:26850000-26869200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:26850200-26853000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:26850200-26861800	Weak transcription	Primary B cells from cord blood	blood
14	chr7:26850200-26862600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr7:26850400-26862600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr7:26850400-26863400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr7:26850400-26871400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr7:26851800-26852200	Enhancers	Fetal Lung	lung
19	chr7:26851800-26855800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:26852000-26853000	Weak transcription	Fetal Kidney	kidney

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