Variant report

Variant	rs588100
Chromosome Location	chr6:75862473-75862474
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	chr1:11752743..11753331-chr6:75862409..75862909,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11961252	1.00[AMR][1000 genomes]
rs1203221	1.00[AMR][1000 genomes]
rs171262	1.00[AMR][1000 genomes]
rs171266	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs173279	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs181179	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240361	0.84[YRI][hapmap]
rs240362	0.91[YRI][hapmap]
rs240364	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs240372	1.00[AMR][1000 genomes]
rs240373	1.00[AMR][1000 genomes]
rs240391	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs240407	1.00[AMR][1000 genomes]
rs240434	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240436	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240716	1.00[YRI][hapmap]
rs240718	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240739	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs240740	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs240742	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703709	1.00[AMR][1000 genomes]
rs2808192	1.00[AMR][1000 genomes]
rs2998372	1.00[AMR][1000 genomes]
rs34807169	1.00[AMR][1000 genomes]
rs428406	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs471960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs480888	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55862072	1.00[AMR][1000 genomes]
rs578715	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58299431	1.00[AMR][1000 genomes]
rs58347254	1.00[AMR][1000 genomes]
rs598034	0.85[YRI][hapmap]
rs601008	0.86[AFR][1000 genomes]
rs612266	1.00[YRI][hapmap]
rs683406	0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73751107	1.00[AMR][1000 genomes]
rs73751108	1.00[AMR][1000 genomes]
rs73751109	1.00[AMR][1000 genomes]
rs73751816	1.00[AMR][1000 genomes]
rs73751817	1.00[AMR][1000 genomes]
rs73751820	1.00[AMR][1000 genomes]
rs73751824	1.00[AMR][1000 genomes]
rs73751826	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022377	chr6:75762463-75919592	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv538309	chr6:75762463-75919592	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv830697	chr6:75763095-75915029	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv886181	chr6:75852488-75919484	Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75813000-75866200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:75823400-75862600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:75824600-75868200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:75824600-75879600	Weak transcription	Fetal Intestine Small	intestine
5	chr6:75827400-75866000	Weak transcription	Left Ventricle	heart
6	chr6:75838200-75862600	Strong transcription	NHEK	skin
7	chr6:75842000-75865200	Strong transcription	HSMM	muscle
8	chr6:75843200-75864800	Weak transcription	Lung	lung
9	chr6:75853200-75867200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr6:75855800-75865600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:75856600-75864800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:75857400-75863600	Genic enhancers	Osteobl	bone
13	chr6:75859800-75866400	Strong transcription	NHDF-Ad	bronchial
14	chr6:75861400-75863400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:75861400-75867600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:75861600-75862800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr6:75861600-75862800	Strong transcription	Fetal Muscle Leg	muscle
18	chr6:75861800-75866200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:75862000-75862600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:75862000-75864800	Weak transcription	NH-A	brain
21	chr6:75862000-75870200	Weak transcription	Hela-S3	cervix
22	chr6:75862200-75864000	Weak transcription	HMEC	breast
23	chr6:75862200-75864800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr6:75862200-75864800	Strong transcription	NHLF	lung
25	chr6:75862200-75880600	Weak transcription	Fetal Stomach	stomach
26	chr6:75862400-75864000	Weak transcription	Ovary	ovary
27	chr6:75862400-75864200	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:75862400-75864200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:75862400-75864400	Weak transcription	Adipose Nuclei	Adipose
30	chr6:75862400-75864400	Weak transcription	HSMMtube	muscle
31	chr6:75862400-75864800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:75862400-75864800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr6:75862400-75864800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr6:75862400-75867400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:75862400-75880400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:75862400-75881000	Weak transcription	Aorta	Aorta
37	chr6:75862400-75884200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:75862400-75885000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr6:75862400-75885600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:75862400-75888600	Weak transcription	Fetal Intestine Large	intestine
41	chr6:75862400-75889800	Weak transcription	Muscle Satellite Cultured Cells	--

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