Variant report

Variant	rs28928301
Chromosome Location	chr2:113833122-113833123
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	chr2:113827867..113831764-chr2:113833015..113836168,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136697	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1586815	1.00[EUR][1000 genomes]
rs2172189	1.00[EUR][1000 genomes]
rs2248588	1.00[EUR][1000 genomes]
rs2248596	1.00[EUR][1000 genomes]
rs2248600	1.00[EUR][1000 genomes]
rs2248604	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2254511	1.00[TSI][hapmap]
rs28928281	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28928283	1.00[ASW][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28928291	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28928299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28928300	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28928302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28928303	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]
rs28928304	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28928305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28928306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28929168	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28939968	1.00[ASW][hapmap]
rs3099479	1.00[EUR][1000 genomes]
rs315935	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs315937	1.00[EUR][1000 genomes]
rs315938	1.00[EUR][1000 genomes]
rs315940	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs315941	1.00[EUR][1000 genomes]
rs315944	1.00[EUR][1000 genomes]
rs315950	1.00[EUR][1000 genomes]
rs315955	1.00[EUR][1000 genomes]
rs4848315	1.00[EUR][1000 genomes]
rs61134068	1.00[EUR][1000 genomes]
rs6735388	1.00[EUR][1000 genomes]
rs6761821	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72954038	1.00[EUR][1000 genomes]
rs7573950	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs923692	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532471	chr2:113682449-113862981	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1007254	chr2:113726982-113887782	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv535894	chr2:113726982-113887782	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv2881	chr2:113800805-113846597	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28928301	FAM84A	trans	lymphoblastoid	seeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113825800-113839600	Enhancers	HMEC	breast
2	chr2:113826200-113833200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:113830800-113833800	Enhancers	Fetal Muscle Leg	muscle
4	chr2:113831400-113834000	Weak transcription	Stomach Mucosa	stomach
5	chr2:113831800-113833200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr2:113832000-113833800	Enhancers	Fetal Thymus	thymus
7	chr2:113832400-113833200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:113832400-113833200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr2:113832400-113834600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:113832400-113835600	Enhancers	Fetal Intestine Small	intestine
11	chr2:113832600-113834600	Weak transcription	Gastric	stomach
12	chr2:113832600-113835000	Enhancers	Fetal Intestine Large	intestine
13	chr2:113832600-113835800	Weak transcription	Lung	lung
14	chr2:113832800-113834000	Weak transcription	NHEK	skin
15	chr2:113832800-113835800	Weak transcription	Esophagus	oesophagus
16	chr2:113833000-113833200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:113833000-113834600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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