Variant report

Variant	rs28475451
Chromosome Location	chr7:128990034-128990035
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	chr7:128990034-128990037	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
AHCYL2	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10235589	0.87[AMR][1000 genomes]
rs10264209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10269495	0.87[AMR][1000 genomes]
rs10281269	0.87[AMR][1000 genomes]
rs10480492	1.00[EUR][1000 genomes]
rs1248453	1.00[EUR][1000 genomes]
rs12533108	0.87[AMR][1000 genomes]
rs1405475	0.87[AMR][1000 genomes]
rs1526898	0.87[AMR][1000 genomes]
rs1526899	0.87[AMR][1000 genomes]
rs1549788	0.87[AMR][1000 genomes]
rs1609043	0.87[AMR][1000 genomes]
rs1991645	0.87[AMR][1000 genomes]
rs2052962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2402946	0.87[AMR][1000 genomes]
rs2402947	0.87[AMR][1000 genomes]
rs2566875	0.87[AMR][1000 genomes]
rs2694575	0.87[AMR][1000 genomes]
rs2694583	0.87[AMR][1000 genomes]
rs2694591	0.87[AMR][1000 genomes]
rs2703098	1.00[EUR][1000 genomes]
rs2718085	0.87[AMR][1000 genomes]
rs2718090	0.87[AMR][1000 genomes]
rs2718091	0.87[AMR][1000 genomes]
rs2718097	0.87[AMR][1000 genomes]
rs2718100	0.87[AMR][1000 genomes]
rs2718109	1.00[EUR][1000 genomes]
rs28399138	0.87[AMR][1000 genomes]
rs28437865	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28864519	1.00[AMR][1000 genomes]
rs6467234	0.87[AMR][1000 genomes]
rs6467236	0.87[AMR][1000 genomes]
rs682299	1.00[EUR][1000 genomes]
rs6949882	0.87[AMR][1000 genomes]
rs6950279	0.87[AMR][1000 genomes]
rs7805353	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9641848	0.87[AMR][1000 genomes]
rs9649526	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	nsv525482	chr7:128890812-129045191	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv516498	chr7:128901429-129072024	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv3331483	chr7:128918442-129082887	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv428508	chr7:128946738-129114691	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv608419	chr7:128980494-128996268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128965400-128994600	Weak transcription	Primary B cells from cord blood	blood
2	chr7:128965800-128995800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr7:128973400-128991000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:128975000-129002600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:128979600-128991400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:128981400-128991200	Weak transcription	A549	lung
7	chr7:128981600-128992000	Weak transcription	Primary T cells from cord blood	blood
8	chr7:128981600-128994400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:128981600-128995400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:128981600-128999200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:128981800-128994600	Weak transcription	Brain Anterior Caudate	brain
12	chr7:128982000-128993400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:128982200-128991200	Weak transcription	Stomach Mucosa	stomach
14	chr7:128982800-128991000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr7:128983400-128992200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr7:128983400-128998600	Weak transcription	Fetal Intestine Large	intestine
17	chr7:128984200-128997000	Weak transcription	Psoas Muscle	Psoas
18	chr7:128984600-128995400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:128984600-129007800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:128986400-128991000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:128986600-128991000	Weak transcription	GM12878-XiMat	blood
22	chr7:128989200-128996600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr7:128989200-129044200	Weak transcription	Ovary	ovary
24	chr7:128989800-128990200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:128989800-128991000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr7:128989800-128991400	Enhancers	NHEK	skin
27	chr7:128990000-128990200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr7:128990000-128993800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:128990000-128995200	Weak transcription	Liver	Liver

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