Variant report

Variant	rs17023092
Chromosome Location	chr1:119574453-119574454
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	chr1:119573691..119576656-chr1:119577479..119579869,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17023108	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17023118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17023129	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17023211	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17023317	1.00[AMR][1000 genomes]
rs17023323	1.00[AMR][1000 genomes]
rs2810933	0.86[ASW][hapmap]
rs56083438	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57667302	1.00[AMR][1000 genomes]
rs60375409	1.00[AMR][1000 genomes]
rs74112264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74112272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74112284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74112509	1.00[AMR][1000 genomes]
rs74112511	1.00[AMR][1000 genomes]
rs74112512	1.00[AMR][1000 genomes]
rs74114807	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74114819	1.00[AMR][1000 genomes]
rs74114822	1.00[AMR][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	esv3494191	chr1:118772550-119719548	Enhancers Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking 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	40 gene(s)	inside rSNPs	diseases
2	esv3494192	chr1:118772550-119719548	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv997707	chr1:119199568-119595949	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119552000-119574800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:119552200-119575200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:119552400-119576600	Weak transcription	HSMMtube	muscle
4	chr1:119559600-119575200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:119560000-119575400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:119560600-119574800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr1:119560600-119575600	Weak transcription	Esophagus	oesophagus
8	chr1:119561000-119575400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:119562200-119575600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:119563000-119575000	Weak transcription	Ovary	ovary
11	chr1:119563200-119575000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr1:119563600-119581200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr1:119565600-119575400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:119568200-119585400	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:119568200-119611200	Weak transcription	Hela-S3	cervix
16	chr1:119568400-119578600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:119569600-119574600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:119569600-119575200	Weak transcription	Right Ventricle	heart
19	chr1:119569600-119587200	Weak transcription	Fetal Intestine Small	intestine
20	chr1:119569600-119589400	Weak transcription	Psoas Muscle	Psoas
21	chr1:119569800-119575600	Weak transcription	Aorta	Aorta
22	chr1:119570000-119586600	Weak transcription	Spleen	Spleen
23	chr1:119570400-119575600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:119570600-119574800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:119570600-119582400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:119570600-119589200	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:119570600-119589600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:119570800-119583200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:119571000-119575400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr1:119571000-119582800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:119571000-119582800	Weak transcription	HMEC	breast
32	chr1:119571000-119582800	Weak transcription	NHEK	skin
33	chr1:119571000-119583400	Weak transcription	HSMM	muscle
34	chr1:119571000-119589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:119571200-119574800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:119571200-119584600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:119571200-119585000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:119571200-119589400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:119571400-119575200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:119571400-119613200	Weak transcription	Pancreas	Pancrea
41	chr1:119571600-119588200	Weak transcription	Fetal Intestine Large	intestine
42	chr1:119571600-119602200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:119571800-119575200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr1:119571800-119577600	Weak transcription	Brain Substantia Nigra	brain
45	chr1:119571800-119589000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:119571800-119612400	Weak transcription	Gastric	stomach
47	chr1:119572000-119586800	Weak transcription	Stomach Mucosa	stomach
48	chr1:119572200-119589400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:119572600-119589200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:119572800-119576800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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