Variant report

Variant	rs6656799
Chromosome Location	chr1:85664965-85664966
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	chr1:85664620..85668785-chr1:85722586..85726821,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162642	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11161540	1.00[AMR][1000 genomes]
rs11161568	1.00[EUR][1000 genomes]
rs12065571	1.00[AMR][1000 genomes]
rs12070991	1.00[AMR][1000 genomes]
rs12084022	1.00[AMR][1000 genomes]
rs12090608	1.00[AMR][1000 genomes]
rs1554596	1.00[EUR][1000 genomes]
rs17121967	1.00[EUR][1000 genomes]
rs17122190	1.00[AMR][1000 genomes]
rs17122301	0.85[AFR][1000 genomes]
rs17122993	0.85[AFR][1000 genomes]
rs17123636	0.84[AFR][1000 genomes]
rs58278399	1.00[EUR][1000 genomes]
rs59078755	1.00[EUR][1000 genomes]
rs61753571	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61753572	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61753619	1.00[AMR][1000 genomes]
rs6663475	1.00[AMR][1000 genomes]
rs6664025	1.00[AMR][1000 genomes]
rs6664273	1.00[AMR][1000 genomes]
rs6667700	1.00[AMR][1000 genomes]
rs6670564	1.00[EUR][1000 genomes]
rs72952681	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv1792086	chr1:85644478-85667608	Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv546701	chr1:85662851-85667386	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv546702	chr1:85663699-85667356	Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv1800754	chr1:85663699-85667557	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv1801195	chr1:85663699-85667608	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv1811802	chr1:85663699-85667608	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	esv1812785	chr1:85663699-85667608	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	esv3447387	chr1:85664874-85665415	Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85615800-85665800	Weak transcription	Esophagus	oesophagus
2	chr1:85639000-85665400	Weak transcription	Placenta	Placenta
3	chr1:85646600-85665200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr1:85648400-85665200	Weak transcription	Ovary	ovary
5	chr1:85648400-85665200	Weak transcription	HSMM	muscle
6	chr1:85649200-85665800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:85654000-85665600	Weak transcription	Brain Anterior Caudate	brain
8	chr1:85654400-85665600	Weak transcription	Brain Substantia Nigra	brain
9	chr1:85654400-85665800	Weak transcription	Gastric	stomach
10	chr1:85654400-85665800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:85654800-85665600	Weak transcription	Pancreas	Pancrea
12	chr1:85656000-85665600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:85656200-85665800	Weak transcription	Lung	lung
14	chr1:85656400-85665200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:85656400-85665400	Weak transcription	HSMMtube	muscle
16	chr1:85656400-85665600	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr1:85661000-85669000	Active TSS	Stomach Smooth Muscle	stomach
18	chr1:85661400-85668400	Active TSS	Colon Smooth Muscle	Colon
19	chr1:85661600-85665200	Weak transcription	GM12878-XiMat	blood
20	chr1:85661800-85665600	Weak transcription	Brain Angular Gyrus	brain
21	chr1:85661800-85665800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:85662200-85665400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:85662200-85665400	Weak transcription	NHDF-Ad	bronchial
24	chr1:85662200-85665800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:85663000-85665800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:85663000-85666200	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr1:85663200-85666200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:85663400-85666000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:85663600-85665200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr1:85663600-85665800	Active TSS	Rectal Smooth Muscle	rectum
31	chr1:85663600-85666200	Active TSS	Right Ventricle	heart
32	chr1:85663600-85666400	Active TSS	Right Atrium	heart
33	chr1:85663600-85668600	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr1:85663800-85665200	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:85663800-85665400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:85663800-85665400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr1:85663800-85665600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:85663800-85667600	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr1:85663800-85667800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:85663800-85667800	Active TSS	K562	blood
41	chr1:85663800-85668000	Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr1:85663800-85668200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:85663800-85668200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:85663800-85668600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:85664000-85665200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr1:85664000-85665600	Active TSS	Fetal Lung	lung
47	chr1:85664000-85667800	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:85664000-85668200	Active TSS	Fetal Intestine Large	intestine
49	chr1:85664200-85665000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
50	chr1:85664200-85665200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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