Variant report

Variant	rs6486398
Chromosome Location	chr11:17843517-17843518
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	chr11:17842186..17845184-chr11:17848108..17850179,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1005008	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10160556	0.84[EUR][1000 genomes]
rs10466421	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10766440	0.84[EUR][1000 genomes]
rs10832860	0.81[EUR][1000 genomes]
rs11024415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11821847	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1548528	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2079227	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2107427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2158395	0.80[CHB][hapmap]
rs2158396	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237943	0.92[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2237944	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2237946	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2237948	0.96[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2237949	0.93[YRI][hapmap]
rs2237950	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2237952	0.85[EUR][1000 genomes]
rs2283249	0.80[CHB][hapmap]
rs2299632	0.80[CHB][hapmap]
rs3802969	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs4757589	0.84[CEU][hapmap]
rs4757591	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs4757593	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6486399	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7106840	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs7109837	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7115183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7124199	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs718439	0.96[CEU][hapmap];0.90[CHB][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs765989	1.00[CEU][hapmap];0.81[CHB][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7929668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7932686	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7935967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832078	chr11:17780503-17953521	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1043973	chr11:17781560-17869896	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17806800-17867400	Weak transcription	Primary B cells from cord blood	blood
2	chr11:17808200-17861400	Weak transcription	Thymus	Thymus
3	chr11:17831200-17849400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr11:17832000-17849600	Weak transcription	Primary T cells from cord blood	blood
5	chr11:17833000-17843800	Weak transcription	HSMMtube	muscle
6	chr11:17833800-17867400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:17835000-17849600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr11:17835000-17869400	Weak transcription	Fetal Intestine Small	intestine
9	chr11:17835200-17884200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr11:17838400-17971600	Weak transcription	Gastric	stomach
11	chr11:17838600-17843600	Weak transcription	Ovary	ovary
12	chr11:17838600-17851000	Weak transcription	Fetal Kidney	kidney
13	chr11:17838800-17860800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:17842400-17844600	Enhancers	Psoas Muscle	Psoas
15	chr11:17842400-17845200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr11:17842600-17843800	Enhancers	Aorta	Aorta
17	chr11:17842600-17844400	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr11:17843000-17844200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:17843000-17844400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr11:17843000-17844400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:17843000-17844400	Enhancers	Fetal Heart	heart
22	chr11:17843000-17844600	Enhancers	NHDF-Ad	bronchial
23	chr11:17843000-17845000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:17843000-17845200	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr11:17843200-17844200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:17843200-17844200	Enhancers	Brain Anterior Caudate	brain
27	chr11:17843200-17844200	Enhancers	Fetal Lung	lung
28	chr11:17843200-17844400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:17843200-17844400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:17843200-17844400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:17843200-17844400	Enhancers	Colon Smooth Muscle	Colon
32	chr11:17843200-17844400	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr11:17843200-17844400	Enhancers	Osteobl	bone
34	chr11:17843200-17844600	Enhancers	Stomach Smooth Muscle	stomach
35	chr11:17843200-17844800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr11:17843200-17844800	Enhancers	Rectal Smooth Muscle	rectum
37	chr11:17843200-17845000	Enhancers	Fetal Stomach	stomach
38	chr11:17843400-17843800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr11:17843400-17843800	Enhancers	Brain Angular Gyrus	brain
40	chr11:17843400-17844000	Enhancers	Stomach Mucosa	stomach
41	chr11:17843400-17844200	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr11:17843400-17844200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:17843400-17844200	Enhancers	HSMM	muscle
44	chr11:17843400-17844400	Enhancers	Adipose Nuclei	Adipose
45	chr11:17843400-17844400	Enhancers	Fetal Muscle Leg	muscle
46	chr11:17843400-17844400	Enhancers	Left Ventricle	heart
47	chr11:17843400-17844400	Enhancers	Lung	lung
48	chr11:17843400-17844400	Enhancers	Right Atrium	heart
49	chr11:17843400-17844400	Enhancers	Right Ventricle	heart
50	chr11:17843400-17844400	Enhancers	NHLF	lung

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