Variant report

Variant	rs2082365
Chromosome Location	chr7:26835945-26835946
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: 164 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10085721	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10227140	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10227231	1.00[CHB][hapmap]
rs10227673	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs10227898	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs10231161	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10239608	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10242572	1.00[CHB][hapmap]
rs10242754	0.88[CHB][hapmap]
rs10256250	1.00[CHB][hapmap]
rs10256561	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10256799	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs10261915	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10267950	1.00[CHB][hapmap]
rs10269731	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs10270187	1.00[CHB][hapmap]
rs10272190	1.00[CHB][hapmap]
rs10272457	1.00[CHB][hapmap]
rs10273468	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10276471	1.00[CHB][hapmap]
rs10281261	1.00[CHB][hapmap]
rs10486478	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs10486483	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs10486485	1.00[CHB][hapmap]
rs10951145	0.89[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs10951149	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1123156	1.00[CHB][hapmap]
rs1123157	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1123158	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs11770043	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs11772673	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs11773029	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs12532796	1.00[CHB][hapmap]
rs12534899	1.00[CHB][hapmap]
rs12535784	1.00[CHB][hapmap]
rs12536560	1.00[CHB][hapmap]
rs12537323	1.00[CHB][hapmap]
rs12540388	1.00[CHB][hapmap]
rs12700755	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12700759	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12700761	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs13186	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs13229947	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs13234201	0.90[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs13234336	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1327988	0.83[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap]
rs1327989	1.00[CHB][hapmap]
rs13438513	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs13438514	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs1468203	1.00[CHB][hapmap]
rs1548478	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1548479	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1548481	1.00[CHB][hapmap]
rs17315775	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs17315929	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs17323934	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs17372780	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs1859101	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2015543	0.86[CEU][hapmap]
rs2023819	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2030136	1.00[CHB][hapmap]
rs2031811	1.00[CHB][hapmap]
rs2106905	1.00[CHB][hapmap]
rs212842	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs212844	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs212846	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs212847	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs212850	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs212852	1.00[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs212853	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs212857	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs212858	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2189016	1.00[CHB][hapmap]
rs2189017	1.00[CHB][hapmap]
rs2189019	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2237328	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2248744	0.86[CHB][hapmap]
rs2253415	0.89[CHB][hapmap]
rs2282906	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs2299102	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs2391360	1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs2391362	1.00[CHB][hapmap]
rs2693665	0.89[CHB][hapmap]
rs2712238	1.00[CHB][hapmap]
rs2712242	1.00[CHB][hapmap]
rs2712246	0.89[CHB][hapmap]
rs2769365	0.82[JPT][hapmap]
rs3757654	1.00[CHB][hapmap]
rs3801803	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs3801805	1.00[CHB][hapmap]
rs3801806	0.82[JPT][hapmap]
rs3801807	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs3801808	1.00[CHB][hapmap]
rs3801810	1.00[CHB][hapmap]
rs3801812	1.00[CHB][hapmap]
rs3801813	1.00[CHB][hapmap]
rs3801814	1.00[CHB][hapmap]
rs3801815	1.00[CHB][hapmap]
rs3801816	1.00[CHB][hapmap]
rs3801819	1.00[CHB][hapmap]
rs3801820	1.00[CHB][hapmap]
rs3801821	1.00[CHB][hapmap]
rs3801825	1.00[CHB][hapmap]
rs3801827	1.00[CHB][hapmap]
rs3801828	1.00[CHB][hapmap]
rs3801830	1.00[CHB][hapmap]
rs3801840	1.00[CHB][hapmap]
rs3801842	1.00[CHB][hapmap]
rs3801843	0.82[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap]
rs3801844	0.83[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap]
rs3801846	0.89[CHB][hapmap];0.90[JPT][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs3801848	1.00[CHB][hapmap]
rs3801850	1.00[CHB][hapmap]
rs3801853	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3801857	1.00[CHB][hapmap]
rs3801860	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3801864	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3823932	1.00[CHB][hapmap]
rs3823933	1.00[CHB][hapmap]
rs3823934	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs3823936	1.00[CHB][hapmap]
rs4719877	1.00[CHB][hapmap]
rs4722630	1.00[CHB][hapmap]
rs4722631	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs5012512	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs503110	0.82[JPT][hapmap]
rs570840	0.81[JPT][hapmap]
rs607099	0.82[JPT][hapmap]
rs6461961	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6461962	1.00[CHB][hapmap]
rs6461963	1.00[CHB][hapmap]
rs6461964	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6461965	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6461971	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6461979	1.00[CHB][hapmap]
rs667841	0.82[JPT][hapmap]
rs6948657	1.00[CHB][hapmap]
rs6951065	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs6964094	1.00[CHB][hapmap]
rs6964817	1.00[CHB][hapmap]
rs6970591	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6971397	1.00[CHB][hapmap]
rs6972378	1.00[CHB][hapmap]
rs6973237	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs727449	1.00[CHB][hapmap]
rs727450	1.00[CHB][hapmap]
rs7457076	1.00[CHB][hapmap]
rs763616	1.00[CHB][hapmap]
rs7785832	1.00[CHB][hapmap]
rs7791513	1.00[CHB][hapmap]
rs7795074	1.00[CHB][hapmap]
rs7799888	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap]
rs7803699	1.00[CHB][hapmap]
rs7804356	1.00[CHB][hapmap];0.81[CHD][hapmap]
rs7805766	1.00[CHB][hapmap]
rs7807640	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs7810109	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7810127	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs891876	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap]
rs9648020	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs989250	1.00[CHB][hapmap];0.90[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
rs2082365	SKAP2	Cis_1M	lymphoblastoid	RTeQTL
rs2082365	SKAP2	cis	parietal	SCAN
rs2082365	C7orf31	cis	parietal	SCAN
rs2082365	HOXA3	cis	cerebellum	SCAN
rs2082365	SKAP2	cis	cerebellum	SCAN

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	chr7:26812400-26849000	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr7:26812800-26841600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr7:26813000-26871200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr7:26821000-26843000	Weak transcription	Fetal Lung	lung
6	chr7:26823000-26846400	Weak transcription	Primary B cells from peripheral blood	blood
7	chr7:26823400-26839600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr7:26825600-26837400	Weak transcription	Lung	lung
10	chr7:26827600-26836800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:26833800-26836600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr7:26834400-26838600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:26834600-26837400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:26834600-26839000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:26834600-26841600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr7:26835200-26836200	Strong transcription	Primary B cells from cord blood	blood
17	chr7:26835400-26840200	Weak transcription	Right Atrium	heart
18	chr7:26835600-26836600	Weak transcription	Fetal Intestine Small	intestine

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