Variant report

Variant	rs348866
Chromosome Location	chr3:100992385-100992386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10936607	0.83[ASN][1000 genomes]
rs13087404	0.83[ASN][1000 genomes]
rs13089177	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13089552	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1471738	0.85[TSI][hapmap]
rs2141180	0.83[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap];0.80[ASN][1000 genomes]
rs2250611	0.83[ASN][1000 genomes]
rs2317699	0.83[ASN][1000 genomes]
rs2317700	0.81[ASN][1000 genomes]
rs2317745	0.83[ASN][1000 genomes]
rs2317749	0.83[ASW][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs2317751	0.83[ASN][1000 genomes]
rs2433031	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2553416	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs2553424	0.81[ASN][1000 genomes]
rs2553427	0.83[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs2553430	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs2682384	0.83[ASN][1000 genomes]
rs2682386	0.83[ASW][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs2682390	0.83[ASN][1000 genomes]
rs2682391	0.83[ASN][1000 genomes]
rs348869	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4683899	0.83[ASN][1000 genomes]
rs4683900	0.83[ASW][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs473702	0.83[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs487623	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs497953	0.83[ASW][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.83[ASN][1000 genomes]
rs503734	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs508537	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs520558	0.83[ASN][1000 genomes]
rs533852	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[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];0.99[ASN][1000 genomes]
rs551442	0.83[ASN][1000 genomes]
rs56075912	0.83[ASN][1000 genomes]
rs62280667	0.83[ASN][1000 genomes]
rs6441602	0.83[ASN][1000 genomes]
rs6441608	0.83[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap];0.80[ASN][1000 genomes]
rs6773536	0.83[ASN][1000 genomes]
rs9816469	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9843186	0.80[ASN][1000 genomes]
rs9859077	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9870114	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv877222	chr3:100715576-101038297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs348866	IMPG2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100954800-100992600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr3:100955000-100994000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr3:100958800-101012800	Weak transcription	Left Ventricle	heart
4	chr3:100975400-100997800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:100979600-100995000	Weak transcription	Aorta	Aorta
6	chr3:100980800-100998000	Weak transcription	HSMM	muscle
7	chr3:100982400-100998800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:100985800-100992400	Weak transcription	Ovary	ovary
9	chr3:100985800-100995400	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:100986600-100998400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:100987200-100994000	Weak transcription	Adipose Nuclei	Adipose
12	chr3:100987400-100993600	Weak transcription	Psoas Muscle	Psoas
13	chr3:100987800-100992800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr3:100988400-100998000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:100989400-101018600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:100990600-100993000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:100991200-100994000	Weak transcription	Gastric	stomach
18	chr3:100991200-100994000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:100991600-100993400	Weak transcription	Pancreas	Pancrea
20	chr3:100991600-100994200	Weak transcription	Primary T cells from cord blood	blood
21	chr3:100991800-100993400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:100991800-100998200	Weak transcription	HSMMtube	muscle

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