Variant report

Variant	rs17012122
Chromosome Location	chr4:87777015-87777016
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87769723..87774057-chr4:87775131..87777452,3	MCF-7	breast:
2	chr4:87776224..87780188-chr4:87811150..87813505,4	MCF-7	breast:
3	chr4:87755836..87758517-chr4:87776083..87778116,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163633	Chromatin interaction
ENSG00000145283	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11937088	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11938345	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6823793	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7687489	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1013308	chr4:87769694-87870168	Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17012122	AFF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87769800-87778600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:87770400-87778600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:87771600-87785600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:87775800-87779200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:87776200-87778800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:87776200-87779000	Enhancers	HMEC	breast
7	chr4:87776200-87779200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:87776200-87779600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:87776400-87779200	Enhancers	NHEK	skin
10	chr4:87776400-87779600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr4:87776600-87777200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
12	chr4:87776600-87778000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:87776600-87779000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:87776800-87777200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr4:87776800-87777200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:87776800-87777200	Enhancers	Osteobl	bone
17	chr4:87776800-87777400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:87776800-87778200	Enhancers	NHDF-Ad	bronchial
19	chr4:87776800-87778600	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr4:87776800-87778800	Enhancers	Hela-S3	cervix
21	chr4:87777000-87777200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
22	chr4:87777000-87778600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr4:87777000-87778600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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