Variant report

Variant	rs2079978
Chromosome Location	chr7:140745149-140745150
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10215245	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1044927	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1089264	0.95[ASN][1000 genomes]
rs10952364	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12538296	0.81[EUR][1000 genomes]
rs12703284	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13234490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236704	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533933	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961288	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2688430	0.95[ASN][1000 genomes]
rs3805116	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs38715	1.00[CHB][hapmap]
rs38720	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs38722	1.00[CHB][hapmap]
rs38723	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs38726	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs38730	0.89[ASN][1000 genomes]
rs38731	0.89[ASN][1000 genomes]
rs38734	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs38736	0.91[ASN][1000 genomes]
rs38739	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs38740	1.00[CHB][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs4726196	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4726225	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs488795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs490810	0.87[ASN][1000 genomes]
rs512177	0.91[ASN][1000 genomes]
rs512509	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs528957	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs533441	0.91[ASN][1000 genomes]
rs544081	0.89[ASN][1000 genomes]
rs545121	0.91[ASN][1000 genomes]
rs557962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs569584	0.89[ASN][1000 genomes]
rs579518	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6464217	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6464260	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6464284	0.87[ASN][1000 genomes]
rs6662	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6967214	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6971577	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7792447	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7801518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs801117	0.95[ASN][1000 genomes]
rs801121	0.95[ASN][1000 genomes]
rs801127	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs801155	0.89[ASN][1000 genomes]
rs801159	0.91[ASN][1000 genomes]
rs9274	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030195	chr7:140615828-140746345	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2079978	CLEC5A	cis	cerebellum	SCAN
rs2079978	MRPS33	Cis_1M	lymphoblastoid	RTeQTL
rs2079978	IFI16	trans	cerebellum	SCAN
rs2079978	YIPF5	trans	cerebellum	SCAN
rs2079978	ADCK2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140742800-140745400	Enhancers	A549	lung
2	chr7:140743400-140745600	Enhancers	Osteobl	bone
3	chr7:140744000-140749000	Weak transcription	HSMMtube	muscle
4	chr7:140744800-140745600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:140745000-140745400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:140745000-140745400	Enhancers	Rectal Smooth Muscle	rectum
7	chr7:140745000-140745600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:140745000-140745600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:140745000-140746400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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