Variant report

Variant	rs11239545
Chromosome Location	chr10:46012245-46012246
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:46010308..46013233-chr10:46016249..46018005,2	MCF-7	breast:
2	chr10:46009283..46011028-chr10:46011723..46015001,3	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10466245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793620	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs10900221	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900224	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900229	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10900230	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10900232	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs11239528	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239532	0.85[CHD][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11239535	0.83[GIH][hapmap]
rs11239536	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239538	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239541	0.81[CEU][hapmap]
rs11239549	0.94[EUR][1000 genomes]
rs11239550	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs11239551	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11239569	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11239571	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12242611	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12243153	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246131	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249012	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257537	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12257549	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12269403	0.96[ASN][1000 genomes]
rs2291428	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291429	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2310783	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs3802548	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3891524	0.81[AFR][1000 genomes]
rs55665473	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56145077	0.80[AFR][1000 genomes]
rs58865519	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59390133	0.93[ASN][1000 genomes]
rs61854096	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854123	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61854156	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7076198	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796498	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs752059	0.85[AFR][1000 genomes]
rs970548	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS 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
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1043536	chr10:45915941-46076235	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv895111	chr10:45989745-46071900	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45989200-46015200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:45999000-46025600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr10:46000800-46019800	Weak transcription	Primary B cells from cord blood	blood
4	chr10:46005000-46025200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr10:46005400-46029800	Weak transcription	Fetal Kidney	kidney
6	chr10:46007600-46021600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr10:46007800-46027400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr10:46008400-46027200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr10:46008800-46021800	Weak transcription	Spleen	Spleen
10	chr10:46009000-46021000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr10:46009200-46015200	Weak transcription	Aorta	Aorta
12	chr10:46009400-46044400	Weak transcription	Thymus	Thymus
13	chr10:46010000-46012800	Weak transcription	Psoas Muscle	Psoas
14	chr10:46010000-46015000	Weak transcription	Ovary	ovary
15	chr10:46010000-46021600	Weak transcription	Right Atrium	heart
16	chr10:46010000-46027800	Weak transcription	Lung	lung
17	chr10:46010000-46056000	Weak transcription	Esophagus	oesophagus
18	chr10:46010200-46027200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr10:46010200-46028800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr10:46010600-46013800	Weak transcription	Adipose Nuclei	Adipose
21	chr10:46010600-46015200	Weak transcription	Liver	Liver
22	chr10:46010800-46013400	Weak transcription	K562	blood
23	chr10:46010800-46021600	Weak transcription	Fetal Muscle Leg	muscle
24	chr10:46010800-46025600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr10:46011000-46025400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:46011200-46012800	Weak transcription	Primary T cells from cord blood	blood
27	chr10:46011200-46019200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr10:46011400-46012800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:46011400-46015200	Weak transcription	Pancreas	Pancrea
30	chr10:46011400-46021600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr10:46011400-46027200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:46011600-46012800	Weak transcription	Left Ventricle	heart
33	chr10:46011600-46013200	Weak transcription	Brain Substantia Nigra	brain
34	chr10:46011600-46030200	Weak transcription	HepG2	liver
35	chr10:46011800-46021600	Weak transcription	Brain Hippocampus Middle	brain

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