Variant report

Variant	rs11015540
Chromosome Location	chr10:18962416-18962417
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	chr10:18962334..18963136-chr6:121821481..121822051,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10828973	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014582	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014594	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014660	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014696	1.00[AMR][1000 genomes]
rs11014721	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014733	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11014797	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014800	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014805	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014825	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014831	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11014961	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11014985	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11014990	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015001	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015020	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11015022	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015033	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015034	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015046	0.86[EUR][1000 genomes]
rs11015060	0.86[EUR][1000 genomes]
rs11015065	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015066	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015089	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11015091	0.91[EUR][1000 genomes]
rs11015100	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11015104	0.91[EUR][1000 genomes]
rs11015180	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11015185	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11015366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11015514	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11015519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11015533	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11015592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11492557	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11511205	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11516859	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12354739	1.00[AMR][1000 genomes]
rs12355360	0.89[AMR][1000 genomes]
rs12355664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12355670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12356125	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12356280	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12356286	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12356533	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12357063	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12357123	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12357491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12358173	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12360352	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17620201	0.89[AMR][1000 genomes]
rs17622004	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17622211	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs17622520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4279920	0.91[EUR][1000 genomes]
rs4497294	0.86[EUR][1000 genomes]
rs45452100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4570480	1.00[AMR][1000 genomes];0.86[EUR][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	nsv550042	chr10:18683267-18994583	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer 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	16 gene(s)	inside rSNPs	diseases
2	nsv466762	chr10:18932172-18976659	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv550121	chr10:18932172-18976659	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:18949400-18973200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:18949600-18972000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:18951000-18965800	Weak transcription	Colonic Mucosa	Colon
4	chr10:18951000-18966600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:18951000-18967400	Weak transcription	Esophagus	oesophagus
6	chr10:18951000-18971800	Weak transcription	Spleen	Spleen
7	chr10:18951000-18976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr10:18951200-18964400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr10:18951400-18962800	Weak transcription	Fetal Brain Male	brain
10	chr10:18951400-18973800	Weak transcription	Aorta	Aorta
11	chr10:18954000-18966600	Strong transcription	Dnd41	blood
12	chr10:18954400-18964400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr10:18954400-18967200	Weak transcription	Gastric	stomach
14	chr10:18954400-18969200	Weak transcription	Right Ventricle	heart
15	chr10:18954400-18973400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr10:18954800-18962800	Weak transcription	K562	blood
17	chr10:18954800-18964800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr10:18955000-18972600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr10:18955200-18967600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr10:18955400-18969200	Weak transcription	Brain Angular Gyrus	brain
21	chr10:18955600-18966600	Strong transcription	Primary B cells from cord blood	blood
22	chr10:18955600-18966600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr10:18955600-18968000	Weak transcription	Brain Substantia Nigra	brain
24	chr10:18955800-18966200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr10:18955800-18966600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr10:18956000-18966200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr10:18956000-18966200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr10:18956000-18966600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr10:18956000-18966800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr10:18956000-18970000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr10:18956000-18972200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr10:18956200-18973200	Weak transcription	Small Intestine	intestine
33	chr10:18956400-18962800	Weak transcription	Hela-S3	cervix
34	chr10:18956400-18962800	Weak transcription	HUVEC	blood vessel
35	chr10:18956400-18966800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr10:18956400-18967800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr10:18956600-18963800	Strong transcription	Brain Germinal Matrix	brain
38	chr10:18956600-18964800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr10:18956600-18965000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr10:18956600-18965200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr10:18956800-18962800	Weak transcription	Pancreas	Pancrea
42	chr10:18956800-18963600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr10:18956800-18965400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr10:18956800-18966600	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr10:18956800-18966600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr10:18956800-18966800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr10:18957000-18965200	Strong transcription	Fetal Muscle Leg	muscle
48	chr10:18957000-18966600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr10:18957200-18965000	Strong transcription	HepG2	liver
50	chr10:18957200-18966200	Strong transcription	Duodenum Mucosa	Duodenum

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