Variant report

Variant	rs9404054
Chromosome Location	chr6:101256597-101256598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101253793..101256720-chr6:101258075..101261197,3	MCF-7	breast:

Extended variants
information (count: 177 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10223467	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1039030	0.92[EUR][1000 genomes]
rs10457077	0.92[EUR][1000 genomes]
rs10457844	0.92[EUR][1000 genomes]
rs10457849	0.94[EUR][1000 genomes]
rs1070990	0.95[EUR][1000 genomes]
rs10872628	0.92[EUR][1000 genomes]
rs10872634	0.92[EUR][1000 genomes]
rs1099916	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11155596	0.82[EUR][1000 genomes]
rs11155606	0.82[EUR][1000 genomes]
rs11155610	0.82[EUR][1000 genomes]
rs11155613	0.86[EUR][1000 genomes]
rs11155618	0.92[EUR][1000 genomes]
rs11155623	0.90[EUR][1000 genomes]
rs11155635	0.92[EUR][1000 genomes]
rs11155636	0.93[EUR][1000 genomes]
rs11155637	0.93[EUR][1000 genomes]
rs11155638	0.93[EUR][1000 genomes]
rs11155653	0.94[EUR][1000 genomes]
rs11155659	0.94[EUR][1000 genomes]
rs11155666	0.94[EUR][1000 genomes]
rs11155673	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11752659	0.93[EUR][1000 genomes]
rs11967951	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12174806	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12175456	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12193960	0.82[EUR][1000 genomes]
rs12195369	0.93[EUR][1000 genomes]
rs12199888	0.82[EUR][1000 genomes]
rs12201852	0.81[EUR][1000 genomes]
rs12202621	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12206838	0.91[EUR][1000 genomes]
rs12207086	0.82[EUR][1000 genomes]
rs12210255	0.92[EUR][1000 genomes]
rs12210550	0.93[EUR][1000 genomes]
rs12212435	0.92[EUR][1000 genomes]
rs12212736	0.82[EUR][1000 genomes]
rs12213201	0.92[EUR][1000 genomes]
rs12214151	0.82[EUR][1000 genomes]
rs12215909	0.88[EUR][1000 genomes]
rs12216199	0.82[EUR][1000 genomes]
rs12216304	0.85[EUR][1000 genomes]
rs12525818	0.80[ASN][1000 genomes]
rs12528607	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12664626	0.92[EUR][1000 genomes]
rs13196803	0.92[EUR][1000 genomes]
rs13208757	0.81[EUR][1000 genomes]
rs13217436	0.83[ASN][1000 genomes]
rs1336242	0.85[EUR][1000 genomes]
rs1336244	0.93[EUR][1000 genomes]
rs1336245	0.92[EUR][1000 genomes]
rs1414734	0.87[EUR][1000 genomes]
rs151572	0.81[EUR][1000 genomes]
rs151637	0.81[EUR][1000 genomes]
rs2036052	0.82[EUR][1000 genomes]
rs2050549	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2132168	0.92[EUR][1000 genomes]
rs2132169	0.92[EUR][1000 genomes]
rs239189	0.81[EUR][1000 genomes]
rs239197	0.81[EUR][1000 genomes]
rs239201	0.81[EUR][1000 genomes]
rs239203	0.81[EUR][1000 genomes]
rs239204	0.81[EUR][1000 genomes]
rs239206	0.81[EUR][1000 genomes]
rs239207	0.80[EUR][1000 genomes]
rs239211	0.81[EUR][1000 genomes]
rs239216	0.82[EUR][1000 genomes]
rs239217	0.82[EUR][1000 genomes]
rs239219	0.81[EUR][1000 genomes]
rs239221	0.81[EUR][1000 genomes]
rs239222	0.81[EUR][1000 genomes]
rs239223	0.81[EUR][1000 genomes]
rs239226	0.81[EUR][1000 genomes]
rs239227	0.81[EUR][1000 genomes]
rs239229	0.81[EUR][1000 genomes]
rs239230	0.81[EUR][1000 genomes]
rs239231	0.81[EUR][1000 genomes]
rs239232	0.81[EUR][1000 genomes]
rs239235	0.80[EUR][1000 genomes]
rs34759265	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35168784	0.91[EUR][1000 genomes]
rs35967345	0.92[EUR][1000 genomes]
rs3811078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4463266	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4571568	0.94[EUR][1000 genomes]
rs4839789	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4839792	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4840147	0.92[EUR][1000 genomes]
rs4840148	0.92[EUR][1000 genomes]
rs4840150	0.86[EUR][1000 genomes]
rs4840151	0.92[EUR][1000 genomes]
rs4840153	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4840154	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4840155	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58266877	0.82[EUR][1000 genomes]
rs62422070	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6570922	0.92[EUR][1000 genomes]
rs6570930	0.92[EUR][1000 genomes]
rs6570969	0.80[ASN][1000 genomes]
rs6570970	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6905113	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6905221	0.82[EUR][1000 genomes]
rs6907240	0.82[EUR][1000 genomes]
rs6909880	0.92[EUR][1000 genomes]
rs6919283	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6919745	0.80[CEU][hapmap]
rs6922219	0.82[EUR][1000 genomes]
rs6925065	0.86[EUR][1000 genomes]
rs6925316	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6925823	0.91[EUR][1000 genomes]
rs6925840	0.94[EUR][1000 genomes]
rs6927598	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6932158	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs6938440	0.82[EUR][1000 genomes]
rs705583	0.95[EUR][1000 genomes]
rs705584	0.95[EUR][1000 genomes]
rs705585	0.95[EUR][1000 genomes]
rs705586	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs723742	0.89[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs723743	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7451736	0.92[EUR][1000 genomes]
rs7740783	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7742011	0.85[EUR][1000 genomes]
rs7746947	0.92[EUR][1000 genomes]
rs7746961	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7747014	0.93[EUR][1000 genomes]
rs7753317	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7754085	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7768210	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846778	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs846799	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs846800	0.95[EUR][1000 genomes]
rs846803	0.95[EUR][1000 genomes]
rs9322173	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9322174	0.93[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9322181	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9322182	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9322183	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9322212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9322213	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9322216	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9373590	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9377214	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9377232	0.80[ASN][1000 genomes]
rs9377234	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9377235	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9386250	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9386257	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390679	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390681	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390685	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9390693	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9390695	0.82[ASN][1000 genomes]
rs9399685	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9399688	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9399694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404016	0.86[EUR][1000 genomes]
rs9404045	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9404049	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9404052	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9404053	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9485410	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9485411	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9498252	0.85[EUR][1000 genomes]
rs9498390	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs964223	0.82[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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101184400-101304600	Weak transcription	Hela-S3	cervix
2	chr6:101191400-101277000	Weak transcription	Esophagus	oesophagus
3	chr6:101212000-101276200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:101212000-101281400	Weak transcription	Aorta	Aorta
5	chr6:101213600-101281600	Weak transcription	Gastric	stomach
6	chr6:101214800-101281600	Weak transcription	Left Ventricle	heart
7	chr6:101215200-101263000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:101215200-101311400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:101215400-101258600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:101223000-101256800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:101226000-101281400	Weak transcription	HUVEC	blood vessel
12	chr6:101233600-101306600	Weak transcription	K562	blood
13	chr6:101233800-101265200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:101234600-101260000	Weak transcription	Brain Hippocampus Middle	brain
15	chr6:101236800-101257800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:101237000-101257400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:101238000-101296200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:101238800-101257200	Weak transcription	HepG2	liver
19	chr6:101239800-101257800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr6:101240200-101257800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:101240400-101266000	Weak transcription	Pancreas	Pancrea
22	chr6:101240600-101277000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:101241600-101276200	Weak transcription	Fetal Intestine Large	intestine
24	chr6:101241800-101276200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:101242600-101262600	Weak transcription	Small Intestine	intestine
26	chr6:101242800-101256800	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:101243200-101257000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:101243200-101276200	Weak transcription	Fetal Lung	lung
29	chr6:101243200-101277800	Weak transcription	NHEK	skin
30	chr6:101243400-101260400	Weak transcription	Fetal Intestine Small	intestine
31	chr6:101243800-101276200	Weak transcription	Thymus	Thymus
32	chr6:101244600-101268800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:101244600-101271000	Weak transcription	HSMMtube	muscle
34	chr6:101244600-101276200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:101244600-101296200	Weak transcription	NH-A	brain
36	chr6:101246000-101257400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:101247000-101263400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:101247600-101257400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:101248200-101259800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:101249400-101298200	Weak transcription	A549	lung
41	chr6:101251400-101271200	Weak transcription	HSMM	muscle
42	chr6:101251600-101256600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:101251600-101260600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:101251800-101258200	Weak transcription	Adipose Nuclei	Adipose
45	chr6:101252200-101293800	Weak transcription	HMEC	breast
46	chr6:101252200-101295600	Weak transcription	NHDF-Ad	bronchial
47	chr6:101253200-101294800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:101253400-101257600	Weak transcription	GM12878-XiMat	blood
49	chr6:101253400-101257800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:101253400-101260400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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