Variant report

Variant	rs9390679
Chromosome Location	chr6:101216102-101216103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 202 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:192)

rs_ID	r²[population]
rs10223467	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1039030	0.94[EUR][1000 genomes]
rs10457077	0.94[EUR][1000 genomes]
rs10457844	0.94[EUR][1000 genomes]
rs10457849	0.94[EUR][1000 genomes]
rs1070990	0.93[EUR][1000 genomes]
rs10872628	0.94[EUR][1000 genomes]
rs10872634	0.94[EUR][1000 genomes]
rs1099916	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11155596	0.84[EUR][1000 genomes]
rs11155606	0.84[EUR][1000 genomes]
rs11155610	0.84[EUR][1000 genomes]
rs11155613	0.88[EUR][1000 genomes]
rs11155618	0.94[EUR][1000 genomes]
rs11155623	0.92[EUR][1000 genomes]
rs11155635	0.94[EUR][1000 genomes]
rs11155636	0.95[EUR][1000 genomes]
rs11155637	0.95[EUR][1000 genomes]
rs11155638	0.95[EUR][1000 genomes]
rs11155653	0.96[EUR][1000 genomes]
rs11155659	0.96[EUR][1000 genomes]
rs11155661	0.81[ASN][1000 genomes]
rs11155666	0.96[EUR][1000 genomes]
rs11155673	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11752659	0.95[EUR][1000 genomes]
rs11758891	0.80[ASN][1000 genomes]
rs11967951	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12174806	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12175456	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193960	0.84[EUR][1000 genomes]
rs12195369	0.95[EUR][1000 genomes]
rs12199888	0.84[EUR][1000 genomes]
rs12201852	0.83[EUR][1000 genomes]
rs12202621	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12206838	0.93[EUR][1000 genomes]
rs12207086	0.84[EUR][1000 genomes]
rs12210255	0.94[EUR][1000 genomes]
rs12210550	0.95[EUR][1000 genomes]
rs12212435	0.94[EUR][1000 genomes]
rs12212736	0.84[EUR][1000 genomes]
rs12213201	0.94[EUR][1000 genomes]
rs12214151	0.84[EUR][1000 genomes]
rs12215909	0.90[EUR][1000 genomes]
rs12216199	0.84[EUR][1000 genomes]
rs12216304	0.86[EUR][1000 genomes]
rs12525128	0.81[ASN][1000 genomes]
rs12528607	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12530388	0.81[CEU][hapmap]
rs12664626	0.94[EUR][1000 genomes]
rs13196803	0.94[EUR][1000 genomes]
rs13208757	0.83[EUR][1000 genomes]
rs1336242	0.87[EUR][1000 genomes]
rs1336244	0.95[EUR][1000 genomes]
rs1336245	0.94[EUR][1000 genomes]
rs1414734	0.89[EUR][1000 genomes]
rs151572	0.83[EUR][1000 genomes]
rs151573	0.82[EUR][1000 genomes]
rs151637	0.83[EUR][1000 genomes]
rs17794439	0.81[ASN][1000 genomes]
rs2036052	0.84[EUR][1000 genomes]
rs2050549	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2101814	0.82[ASN][1000 genomes]
rs2132168	0.94[EUR][1000 genomes]
rs2132169	0.94[EUR][1000 genomes]
rs2134044	0.80[ASN][1000 genomes]
rs239189	0.83[EUR][1000 genomes]
rs239190	0.82[EUR][1000 genomes]
rs239197	0.83[EUR][1000 genomes]
rs239201	0.83[EUR][1000 genomes]
rs239203	0.83[EUR][1000 genomes]
rs239204	0.83[EUR][1000 genomes]
rs239206	0.83[EUR][1000 genomes]
rs239207	0.82[EUR][1000 genomes]
rs239211	0.83[EUR][1000 genomes]
rs239216	0.84[EUR][1000 genomes]
rs239217	0.84[EUR][1000 genomes]
rs239219	0.83[EUR][1000 genomes]
rs239221	0.83[EUR][1000 genomes]
rs239222	0.83[EUR][1000 genomes]
rs239223	0.83[EUR][1000 genomes]
rs239226	0.83[EUR][1000 genomes]
rs239227	0.83[EUR][1000 genomes]
rs239229	0.83[EUR][1000 genomes]
rs239230	0.83[EUR][1000 genomes]
rs239231	0.83[EUR][1000 genomes]
rs239232	0.83[EUR][1000 genomes]
rs239235	0.82[EUR][1000 genomes]
rs239237	0.82[EUR][1000 genomes]
rs239238	0.82[EUR][1000 genomes]
rs239239	0.82[EUR][1000 genomes]
rs239242	0.82[EUR][1000 genomes]
rs239245	0.82[EUR][1000 genomes]
rs239246	0.82[EUR][1000 genomes]
rs239247	0.82[EUR][1000 genomes]
rs239248	0.81[EUR][1000 genomes]
rs239249	0.82[EUR][1000 genomes]
rs240143	0.82[EUR][1000 genomes]
rs240145	0.82[EUR][1000 genomes]
rs240146	0.82[EUR][1000 genomes]
rs240154	0.82[EUR][1000 genomes]
rs34759265	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35168784	0.93[EUR][1000 genomes]
rs35967345	0.94[EUR][1000 genomes]
rs369125	0.81[EUR][1000 genomes]
rs3811078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818233	0.80[ASN][1000 genomes]
rs4463266	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4571568	0.96[EUR][1000 genomes]
rs4839789	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4839792	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4840147	0.94[EUR][1000 genomes]
rs4840148	0.94[EUR][1000 genomes]
rs4840150	0.88[EUR][1000 genomes]
rs4840151	0.94[EUR][1000 genomes]
rs4840153	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4840154	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4840155	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58266877	0.84[EUR][1000 genomes]
rs62422070	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6570922	0.94[EUR][1000 genomes]
rs6570930	0.94[EUR][1000 genomes]
rs6570970	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6905113	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905221	0.84[EUR][1000 genomes]
rs6907240	0.84[EUR][1000 genomes]
rs6909880	0.94[EUR][1000 genomes]
rs6919283	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6919745	0.83[CEU][hapmap]
rs6922219	0.84[EUR][1000 genomes]
rs6925065	0.88[EUR][1000 genomes]
rs6925316	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925823	0.93[EUR][1000 genomes]
rs6925840	0.96[EUR][1000 genomes]
rs6927598	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6932158	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6938440	0.84[EUR][1000 genomes]
rs705583	0.93[EUR][1000 genomes]
rs705584	0.93[EUR][1000 genomes]
rs705585	0.93[EUR][1000 genomes]
rs705586	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs723742	0.89[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs723743	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7451736	0.94[EUR][1000 genomes]
rs7740783	0.97[EUR][1000 genomes]
rs7742011	0.87[EUR][1000 genomes]
rs7746947	0.94[EUR][1000 genomes]
rs7746961	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747014	0.95[EUR][1000 genomes]
rs7753317	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7754085	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759463	0.83[ASN][1000 genomes]
rs7768210	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs846778	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs846799	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs846800	0.93[EUR][1000 genomes]
rs846803	0.93[EUR][1000 genomes]
rs9322173	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322174	0.99[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9322181	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322182	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322183	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9322213	0.95[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9322216	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9373590	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9377193	0.81[ASN][1000 genomes]
rs9377214	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9377234	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9377235	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9386250	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386257	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9390675	0.83[ASN][1000 genomes]
rs9390681	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390682	0.83[ASN][1000 genomes]
rs9390685	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390693	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9399685	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399688	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9399694	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9404016	0.88[EUR][1000 genomes]
rs9404022	0.83[ASN][1000 genomes]
rs9404031	0.83[ASN][1000 genomes]
rs9404033	0.83[ASN][1000 genomes]
rs9404045	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9404049	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9404052	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9404053	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9404054	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9485410	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9485411	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9498252	0.87[EUR][1000 genomes]
rs9498390	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv886445	chr6:101004751-101240763	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv886456	chr6:101049108-101277926	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv604275	chr6:101158950-101277926	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1016353	chr6:101172705-101304041	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1024526	chr6:101192726-101241291	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101184400-101304600	Weak transcription	Hela-S3	cervix
2	chr6:101190800-101216200	Weak transcription	Stomach Mucosa	stomach
3	chr6:101190800-101217400	Weak transcription	NHLF	lung
4	chr6:101191400-101217600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:101191400-101277000	Weak transcription	Esophagus	oesophagus
6	chr6:101207600-101217000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:101208400-101221400	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:101209400-101216600	Weak transcription	Lung	lung
9	chr6:101211800-101216200	Weak transcription	Brain Angular Gyrus	brain
10	chr6:101211800-101216400	Weak transcription	Spleen	Spleen
11	chr6:101211800-101218200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:101211800-101222800	Weak transcription	Fetal Stomach	stomach
13	chr6:101211800-101223400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:101211800-101231800	Weak transcription	Pancreas	Pancrea
15	chr6:101212000-101216600	Weak transcription	Brain Substantia Nigra	brain
16	chr6:101212000-101218000	Weak transcription	Brain Anterior Caudate	brain
17	chr6:101212000-101222600	Weak transcription	NHEK	skin
18	chr6:101212000-101246400	Weak transcription	Psoas Muscle	Psoas
19	chr6:101212000-101276200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:101212000-101281400	Weak transcription	Aorta	Aorta
21	chr6:101212200-101216800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:101212400-101219600	Weak transcription	K562	blood
23	chr6:101212800-101217200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:101213200-101216800	Weak transcription	HepG2	liver
25	chr6:101213200-101227400	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:101213200-101242800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:101213400-101224000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:101213400-101244000	Weak transcription	HSMMtube	muscle
29	chr6:101213600-101216400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:101213600-101216600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:101213600-101217000	Weak transcription	Small Intestine	intestine
32	chr6:101213600-101241600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:101213600-101256000	Weak transcription	Ovary	ovary
34	chr6:101213600-101281600	Weak transcription	Gastric	stomach
35	chr6:101213800-101216200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:101213800-101216800	Weak transcription	Fetal Muscle Leg	muscle
37	chr6:101213800-101216800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:101213800-101217000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:101213800-101224400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:101213800-101237000	Weak transcription	Primary T cells from cord blood	blood
41	chr6:101213800-101250800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:101213800-101254200	Weak transcription	Fetal Thymus	thymus
43	chr6:101214000-101218800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr6:101214000-101218800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:101214600-101216200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:101214600-101216800	Weak transcription	Fetal Intestine Large	intestine
47	chr6:101214600-101216800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr6:101214600-101218800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:101214600-101236400	Weak transcription	GM12878-XiMat	blood
50	chr6:101214800-101217400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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