Variant report

Variant	rs7799888
Chromosome Location	chr7:26839892-26839893
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	chr7:26839409..26841289-chr7:26844837..26847761,2	MCF-7	breast:

Extended variants
information (count: 245 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:242)

rs_ID	r²[population]
rs10085721	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10215738	0.82[AFR][1000 genomes]
rs10224133	0.90[ASN][1000 genomes]
rs10225924	0.81[AFR][1000 genomes]
rs10227140	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10227231	1.00[CHB][hapmap]
rs10227673	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs10227898	1.00[CHB][hapmap]
rs10231161	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10232697	0.87[ASN][1000 genomes]
rs10237921	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10238253	0.93[ASN][1000 genomes]
rs10239608	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241952	0.93[ASN][1000 genomes]
rs10242572	1.00[CHB][hapmap]
rs10245162	0.93[ASN][1000 genomes]
rs10245367	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246641	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247509	0.87[ASN][1000 genomes]
rs10249824	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10250223	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10255249	0.90[ASN][1000 genomes]
rs10256250	1.00[CHB][hapmap]
rs10256561	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256799	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs10261915	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs10263118	0.87[ASN][1000 genomes]
rs10267950	1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs10269731	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10270187	1.00[CHB][hapmap]
rs10272190	1.00[CHB][hapmap]
rs10272303	0.81[AFR][1000 genomes]
rs10272457	1.00[CHB][hapmap]
rs10273468	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs10276471	1.00[CHB][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs10276636	0.87[ASN][1000 genomes]
rs10281261	1.00[CHB][hapmap]
rs1030644	0.87[ASN][1000 genomes]
rs10486478	0.86[CHB][hapmap];0.81[GIH][hapmap]
rs10486483	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs10486485	1.00[CHB][hapmap]
rs10807834	0.86[ASN][1000 genomes]
rs10951145	0.88[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10951149	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1123156	1.00[CHB][hapmap]
rs1123157	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs1123158	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11770043	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11772673	0.84[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11773029	1.00[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs11773050	0.90[ASN][1000 genomes]
rs12532339	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532395	0.81[AFR][1000 genomes]
rs12532796	1.00[CHB][hapmap]
rs12534899	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs12535078	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535784	1.00[CHB][hapmap]
rs12536560	1.00[CHB][hapmap];0.83[YRI][hapmap]
rs12537323	1.00[CHB][hapmap]
rs12540388	1.00[CHB][hapmap]
rs12668948	0.84[ASN][1000 genomes]
rs12700755	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12700758	0.87[ASN][1000 genomes]
rs12700759	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs12700760	0.90[ASN][1000 genomes]
rs12700761	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs13186	1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs13229947	1.00[CHB][hapmap]
rs13234201	0.89[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13234336	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1327988	0.91[ASW][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs1327989	1.00[CHB][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs13438513	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs13438514	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs1468203	1.00[CHB][hapmap]
rs1548478	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1548479	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1548481	1.00[CHB][hapmap]
rs17315775	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs17315929	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs17323934	1.00[CHB][hapmap]
rs17372780	1.00[CHB][hapmap]
rs1859101	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2015543	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2017794	0.87[ASN][1000 genomes]
rs2023819	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2030136	1.00[CHB][hapmap]
rs2031811	1.00[CHB][hapmap]
rs2082365	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]
rs2106905	1.00[CHB][hapmap]
rs212842	1.00[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs212844	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs212846	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs212847	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs212849	0.84[ASN][1000 genomes]
rs212850	1.00[CHB][hapmap]
rs212852	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs212853	1.00[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs212855	0.84[ASN][1000 genomes]
rs212857	1.00[CHB][hapmap]
rs212858	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2189016	1.00[CHB][hapmap]
rs2189017	1.00[CHB][hapmap]
rs2189019	1.00[CHB][hapmap]
rs2237328	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2253415	0.88[CHB][hapmap]
rs2282906	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2299102	1.00[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2391359	0.83[ASN][1000 genomes]
rs2391360	1.00[CHB][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2391362	1.00[CHB][hapmap]
rs2712238	0.84[CHB][hapmap]
rs2712242	1.00[CHB][hapmap]
rs2769365	0.82[JPT][hapmap]
rs28403911	0.93[ASN][1000 genomes]
rs28733208	0.83[AFR][1000 genomes]
rs3757654	1.00[CHB][hapmap]
rs3801803	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs3801805	1.00[CHB][hapmap]
rs3801806	0.82[JPT][hapmap]
rs3801807	0.83[ASW][hapmap];1.00[CHB][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]
rs3801835	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3801840	1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs3801842	1.00[CHB][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801843	0.91[ASW][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801844	0.91[ASW][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs3801846	0.88[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs3801847	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801848	1.00[CHB][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3801850	1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs3801853	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs3801854	0.93[ASN][1000 genomes]
rs3801855	0.93[ASN][1000 genomes]
rs3801857	1.00[CHB][hapmap]
rs3801860	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs3801864	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3801866	0.89[ASN][1000 genomes]
rs3801867	0.89[ASN][1000 genomes]
rs3801868	0.86[ASN][1000 genomes]
rs3823932	1.00[CHB][hapmap]
rs3823933	1.00[CHB][hapmap]
rs3823934	1.00[CHB][hapmap]
rs3823936	1.00[CHB][hapmap]
rs3823939	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4345466	0.93[ASN][1000 genomes]
rs4512299	0.93[ASN][1000 genomes]
rs4573150	0.87[ASN][1000 genomes]
rs4719877	1.00[CHB][hapmap]
rs4719879	0.87[ASN][1000 genomes]
rs4722630	1.00[CHB][hapmap]
rs4722631	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4722633	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4722634	0.87[ASN][1000 genomes]
rs5012512	0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs503110	0.82[JPT][hapmap]
rs55836768	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55904994	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56359409	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs570840	0.81[JPT][hapmap]
rs58988613	0.87[ASN][1000 genomes]
rs607099	0.82[JPT][hapmap]
rs6461961	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs6461962	1.00[CHB][hapmap]
rs6461963	1.00[CHB][hapmap]
rs6461964	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs6461965	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6461971	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6461973	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6461974	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6461975	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6461976	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6461979	1.00[CHB][hapmap]
rs667841	0.82[JPT][hapmap]
rs6943568	0.83[ASN][1000 genomes]
rs6944529	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944926	0.82[LWK][hapmap]
rs6948657	1.00[CHB][hapmap]
rs6951065	1.00[CHB][hapmap]
rs6956088	0.83[AFR][1000 genomes]
rs6964094	1.00[CHB][hapmap]
rs6964817	1.00[CHB][hapmap]
rs6965167	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6970591	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6971397	1.00[CHB][hapmap]
rs6972378	1.00[CHB][hapmap]
rs6973237	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs727449	1.00[CHB][hapmap]
rs727450	0.89[CHB][hapmap]
rs73065517	0.83[AFR][1000 genomes]
rs73065521	0.83[AFR][1000 genomes]
rs73065526	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs744611	0.93[ASN][1000 genomes]
rs744612	0.93[ASN][1000 genomes]
rs7457076	1.00[CHB][hapmap]
rs763616	1.00[CHB][hapmap]
rs7777316	0.87[ASN][1000 genomes]
rs7777744	0.87[ASN][1000 genomes]
rs7779604	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7779843	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784206	0.90[ASN][1000 genomes]
rs7784548	0.87[ASN][1000 genomes]
rs7785832	1.00[CHB][hapmap]
rs7788165	0.84[ASN][1000 genomes]
rs7791513	1.00[CHB][hapmap]
rs7793663	0.93[ASN][1000 genomes]
rs7794399	0.90[ASN][1000 genomes]
rs7795074	1.00[CHB][hapmap]
rs7798696	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802514	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7802852	0.87[ASN][1000 genomes]
rs7803699	1.00[CHB][hapmap]
rs7804356	0.83[ASW][hapmap];1.00[CHB][hapmap]
rs7805766	1.00[CHB][hapmap]
rs7807640	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs7810109	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7810127	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7811764	0.84[ASN][1000 genomes]
rs891874	0.93[ASN][1000 genomes]
rs891875	0.93[ASN][1000 genomes]
rs891876	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs934410	0.93[ASN][1000 genomes]
rs9648018	0.90[ASN][1000 genomes]
rs9648020	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9648021	0.87[ASN][1000 genomes]
rs9648330	0.87[ASN][1000 genomes]
rs9648331	0.85[ASN][1000 genomes]
rs9770851	0.85[ASN][1000 genomes]
rs989250	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][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
rs7799888	SKAP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 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	chr7:26825400-26872400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:26834600-26841600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr7:26835400-26840200	Weak transcription	Right Atrium	heart
10	chr7:26836600-26846200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr7:26837400-26842800	Weak transcription	Primary B cells from cord blood	blood
12	chr7:26839400-26842800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:26839400-26871800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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