Variant report

Variant	rs17829777
Chromosome Location	chr4:102060712-102060713
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102058000..102061139-chr4:102062648..102064879,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13102391	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13120190	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1405688	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17030795	0.80[CEU][hapmap]
rs17829885	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35057231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35170337	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36096364	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71614680	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71614681	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71614682	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71614683	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71614684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102026200-102068600	Weak transcription	Primary T cells from cord blood	blood
2	chr4:102049200-102064800	Weak transcription	HMEC	breast
3	chr4:102056600-102062200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:102057200-102061400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:102057200-102061600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr4:102057200-102061600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:102057400-102062400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr4:102057600-102061400	Weak transcription	Primary B cells from cord blood	blood
9	chr4:102057600-102062200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr4:102057600-102062200	Weak transcription	Left Ventricle	heart
11	chr4:102057600-102062800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:102057600-102063400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:102058000-102061400	Weak transcription	GM12878-XiMat	blood
14	chr4:102058200-102061400	Weak transcription	Stomach Mucosa	stomach
15	chr4:102058400-102061000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:102058400-102063200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:102058600-102063400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr4:102058800-102061000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:102058800-102061600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:102059000-102061400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr4:102059400-102061800	Enhancers	Brain Hippocampus Middle	brain
22	chr4:102059400-102076600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:102059600-102060800	Weak transcription	A549	lung
24	chr4:102059600-102061200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:102059800-102065200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:102060400-102061000	Enhancers	Brain Angular Gyrus	brain
27	chr4:102060600-102060800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr4:102060600-102060800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr4:102060600-102061000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:102060600-102061000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr4:102060600-102061800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:102060600-102062000	Enhancers	Brain Cingulate Gyrus	brain
33	chr4:102060600-102062200	Enhancers	Brain Anterior Caudate	brain

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