Variant report

Variant	rs17023129
Chromosome Location	chr1:119580792-119580793
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	chr1:119580791..119584405-chr1:119681779..119684464,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231365	Chromatin interaction
ENSG00000116874	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs17023092	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]
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]
rs17023211	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][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]
rs2645306	1.00[MEX][hapmap]
rs2810933	0.86[ASW][hapmap];1.00[MEX][hapmap]
rs4600087	1.00[MEX][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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119563600-119581200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr1:119568200-119585400	Weak transcription	Brain Hippocampus Middle	brain
3	chr1:119568200-119611200	Weak transcription	Hela-S3	cervix
4	chr1:119569600-119587200	Weak transcription	Fetal Intestine Small	intestine
5	chr1:119569600-119589400	Weak transcription	Psoas Muscle	Psoas
6	chr1:119570000-119586600	Weak transcription	Spleen	Spleen
7	chr1:119570600-119582400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:119570600-119589200	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:119570600-119589600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:119570800-119583200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:119571000-119582800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:119571000-119582800	Weak transcription	HMEC	breast
13	chr1:119571000-119582800	Weak transcription	NHEK	skin
14	chr1:119571000-119583400	Weak transcription	HSMM	muscle
15	chr1:119571000-119589400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:119571200-119584600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:119571200-119585000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr1:119571200-119589400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:119571400-119613200	Weak transcription	Pancreas	Pancrea
20	chr1:119571600-119588200	Weak transcription	Fetal Intestine Large	intestine
21	chr1:119571600-119602200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:119571800-119589000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:119571800-119612400	Weak transcription	Gastric	stomach
24	chr1:119572000-119586800	Weak transcription	Stomach Mucosa	stomach
25	chr1:119572200-119589400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:119572600-119589200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:119572800-119583600	Weak transcription	Small Intestine	intestine
28	chr1:119572800-119589600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:119573400-119599800	Weak transcription	Fetal Stomach	stomach
30	chr1:119573600-119588000	Weak transcription	Fetal Kidney	kidney
31	chr1:119574000-119587000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr1:119574200-119587000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:119574200-119589600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:119574200-119590000	Weak transcription	Thymus	Thymus
35	chr1:119574400-119588400	Weak transcription	Fetal Lung	lung
36	chr1:119575000-119585800	Weak transcription	Dnd41	blood
37	chr1:119575800-119583600	Weak transcription	Esophagus	oesophagus
38	chr1:119575800-119583800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:119575800-119586600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr1:119575800-119589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:119575800-119592400	Weak transcription	Brain Angular Gyrus	brain
42	chr1:119575800-119603200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:119576000-119586400	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:119576000-119586800	Weak transcription	Liver	Liver
45	chr1:119576000-119587200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:119576000-119588000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:119576000-119588600	Weak transcription	Brain Anterior Caudate	brain
48	chr1:119576000-119588800	Weak transcription	Lung	lung
49	chr1:119576000-119589000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:119576000-119589200	Weak transcription	Aorta	Aorta

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