Variant report

Variant	rs17083167
Chromosome Location	chr4:54462220-54462221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:54462160-54462579	SH-SY5Y	brain:	n/a	n/a
2	EP300	chr4:54462155-54462498	SK-N-SH_RA	brain:	n/a	n/a
3	EP300	chr4:54461903-54462497	SK-N-SH_RA	brain:	n/a	n/a
4	GATA3	chr4:54461983-54462518	SK-N-SH	brain:	n/a	n/a
5	GATA3	chr4:54462005-54462543	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54460125..54463943-chr4:54465847..54469777,4	MCF-7	breast:

Variant related genes	Relation type
LNX1	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1015801	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945428	0.80[ASN][1000 genomes]
rs17083170	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048511	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv437918	chr4:54451175-54483569	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54457600-54464400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:54459400-54462400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:54459600-54463400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:54459600-54465000	Weak transcription	Osteobl	bone
5	chr4:54459600-54465200	Weak transcription	Fetal Muscle Leg	muscle
6	chr4:54459600-54465200	Weak transcription	Right Ventricle	heart
7	chr4:54459600-54465400	Weak transcription	Left Ventricle	heart
8	chr4:54459600-54467400	Weak transcription	Esophagus	oesophagus
9	chr4:54459600-54467400	Weak transcription	Pancreas	Pancrea
10	chr4:54459600-54467400	Weak transcription	Right Atrium	heart
11	chr4:54459800-54464200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:54459800-54464600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:54459800-54464600	Weak transcription	Stomach Mucosa	stomach
14	chr4:54459800-54467400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr4:54460000-54465800	Weak transcription	GM12878-XiMat	blood
16	chr4:54460200-54464600	Weak transcription	Fetal Intestine Small	intestine
17	chr4:54460200-54467400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr4:54460200-54467400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:54460200-54467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:54460800-54464600	Weak transcription	Fetal Intestine Large	intestine
21	chr4:54461200-54462400	Enhancers	HMEC	breast
22	chr4:54461200-54462800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr4:54461200-54463000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr4:54461400-54462800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr4:54461400-54467000	Weak transcription	Placenta	Placenta
26	chr4:54461600-54463400	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr4:54461600-54463600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:54461600-54463800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr4:54461600-54463800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:54461800-54462600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr4:54461800-54462800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr4:54462000-54462400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr4:54462000-54464800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:54462000-54467400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:54462200-54464800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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