Variant report

Variant	rs41406248
Chromosome Location	chr10:28568713-28568714
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	chr10:28566640..28568804-chr10:28569342..28571331,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10763652	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs10763653	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10826426	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10826427	0.87[ASN][1000 genomes]
rs10826428	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10826429	0.87[ASN][1000 genomes]
rs10826430	0.86[ASN][1000 genomes]
rs10826431	0.90[ASN][1000 genomes]
rs10826438	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10826439	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006921	0.89[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11006924	0.87[ASN][1000 genomes]
rs11006930	0.87[ASN][1000 genomes]
rs11006931	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11006932	0.82[ASW][hapmap];0.81[CEU][hapmap]
rs11006935	0.82[ASW][hapmap];0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs11006936	0.83[AMR][1000 genomes]
rs11006940	1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs11006948	0.93[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11006952	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11006953	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11006971	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11006972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11006974	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006975	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006976	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006977	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006979	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11006980	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11006981	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11006982	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11007002	0.87[AFR][1000 genomes]
rs11813709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11814117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12243871	0.87[ASN][1000 genomes]
rs12243947	0.87[ASN][1000 genomes]
rs12247867	0.87[ASN][1000 genomes]
rs12258617	0.87[ASN][1000 genomes]
rs12258912	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12263084	0.86[ASN][1000 genomes]
rs12263807	0.87[ASN][1000 genomes]
rs12264931	0.87[ASN][1000 genomes]
rs12355677	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12356457	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12357214	0.87[ASN][1000 genomes]
rs12357236	0.87[ASN][1000 genomes]
rs12357385	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[AFR][1000 genomes]
rs12357685	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12358399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12358648	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12359569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12359994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1840877	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs1840879	0.87[ASN][1000 genomes]
rs2100614	1.00[YRI][hapmap]
rs2607548	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs2801845	0.81[CEU][hapmap]
rs2985524	0.81[CEU][hapmap]
rs2985525	0.80[CEU][hapmap]
rs2985529	0.81[CEU][hapmap]
rs2985530	0.81[CEU][hapmap]
rs2985533	0.81[CEU][hapmap]
rs2997203	0.81[CEU][hapmap]
rs3847384	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4747617	0.81[CEU][hapmap]
rs55654850	0.90[ASN][1000 genomes]
rs58057536	0.90[ASN][1000 genomes]
rs61845919	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61845921	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61845936	0.96[ASN][1000 genomes]
rs61845938	0.87[AFR][1000 genomes]
rs6481511	0.86[ASN][1000 genomes]
rs6481513	1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs6481514	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7070142	0.86[ASN][1000 genomes]
rs7071331	0.84[ASN][1000 genomes]
rs7072588	0.81[ASN][1000 genomes]
rs7072854	1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7073107	0.80[CEU][hapmap];0.83[AMR][1000 genomes]
rs7078271	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs7078842	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7081371	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7084650	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7084702	0.87[ASN][1000 genomes]
rs7084878	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7085924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7086267	0.87[ASN][1000 genomes]
rs7086807	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7086943	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7090006	0.81[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7090735	0.84[ASN][1000 genomes]
rs7091031	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7091331	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7092706	0.90[ASN][1000 genomes]
rs7094807	0.86[ASN][1000 genomes]
rs7097351	0.87[ASN][1000 genomes]
rs7100335	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7100582	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7100619	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7100983	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7101006	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73608074	0.87[ASN][1000 genomes]
rs74129024	0.83[AMR][1000 genomes]
rs7893685	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7893733	0.86[ASN][1000 genomes]
rs7893878	0.86[ASN][1000 genomes]
rs7893935	0.84[ASN][1000 genomes]
rs7903957	0.81[CEU][hapmap]
rs7914949	0.81[CEU][hapmap]
rs7916525	0.82[ASW][hapmap];0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs7923023	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9664773	1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv1040916	chr10:28558982-28579141	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
6	nsv466856	chr10:28562647-28571860	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv470929	chr10:28562647-28571860	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv550285	chr10:28562647-28571860	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv818752	chr10:28562647-28571860	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv437663	chr10:28562647-28585496	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
11	esv2760125	chr10:28563995-28570599	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1036270	chr10:28563995-28574327	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1045247	chr10:28563995-28574624	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1039546	chr10:28563995-28579141	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
15	esv2421445	chr10:28564207-28571860	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv3693051	chr10:28564732-28571860	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv818753	chr10:28564732-28571860	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv515548	chr10:28564732-28579969	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
19	esv12765	chr10:28564737-28573369	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv514550	chr10:28564750-28569098	Weak transcription Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv442175	chr10:28564760-28569670	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv438167	chr10:28567807-28569959	Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
23	nsv818754	chr10:28567807-28571860	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28550400-28582600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr10:28553000-28570800	Weak transcription	Esophagus	oesophagus
3	chr10:28553400-28569600	Weak transcription	Pancreas	Pancrea
4	chr10:28556200-28570800	Weak transcription	Primary B cells from cord blood	blood
5	chr10:28556400-28571000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:28559600-28570800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:28562600-28570800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:28564000-28573200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:28564200-28569400	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:28564200-28573200	Weak transcription	Primary T cells from cord blood	blood
11	chr10:28564400-28570800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr10:28564800-28570800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr10:28564800-28572800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr10:28564800-28573000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr10:28565000-28571000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:28566200-28571000	Weak transcription	HepG2	liver
17	chr10:28566800-28573000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr10:28567800-28569200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr10:28567800-28570200	Enhancers	Fetal Heart	heart
20	chr10:28568000-28569000	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr10:28568000-28569200	Enhancers	Left Ventricle	heart
22	chr10:28568000-28569200	Enhancers	Psoas Muscle	Psoas
23	chr10:28568200-28568800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr10:28568200-28570800	Weak transcription	Fetal Muscle Leg	muscle
25	chr10:28568400-28570600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr10:28568400-28570800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:28568400-28570800	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr10:28568400-28573200	Weak transcription	Right Ventricle	heart
29	chr10:28568600-28569000	Weak transcription	Stomach Smooth Muscle	stomach

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