Variant report

Variant	rs2596622
Chromosome Location	chr3:24204892-24204893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2596623	0.80[AMR][1000 genomes]
rs2683528	0.81[AMR][1000 genomes]
rs2683529	0.81[AMR][1000 genomes]
rs2683536	0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs62255847	0.81[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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834639	chr3:24037113-24233925	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2596622	PPIL1	trans	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24180000-24206600	Weak transcription	Pancreas	Pancrea
2	chr3:24186200-24230800	Weak transcription	Fetal Intestine Large	intestine
3	chr3:24188200-24210000	Weak transcription	Gastric	stomach
4	chr3:24188200-24215200	Weak transcription	Right Ventricle	heart
5	chr3:24198800-24218800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:24199400-24225800	Weak transcription	Fetal Intestine Small	intestine
7	chr3:24202200-24205000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:24202200-24208000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:24202400-24206200	Weak transcription	Left Ventricle	heart
10	chr3:24202400-24218000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:24202600-24206600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:24203600-24208000	Weak transcription	Ovary	ovary
13	chr3:24203600-24218600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:24203800-24206600	Weak transcription	Aorta	Aorta
15	chr3:24204000-24205000	Weak transcription	Psoas Muscle	Psoas
16	chr3:24204000-24207800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:24204000-24208000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:24204000-24208000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:24204000-24208000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:24204000-24208000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:24204200-24207000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:24204200-24208000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:24204200-24213000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:24204800-24206200	Weak transcription	Liver	Liver
25	chr3:24204800-24207600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:24204800-24208000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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