Variant report

No.	Distal block	Cell Line	Cell type
1	chr3:24464738..24466797-chr3:24486080..24488877,2	K562	blood:
2	chr3:24358624..24360573-chr3:24487137..24489145,2	MCF-7	breast:
3	chr3:24485939..24488891-chr3:24534407..24536534,2	K562	blood:

Variant related genes	Relation type
ENSG00000151090	Chromatin interaction
ENSG00000228791	Chromatin interaction

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10510544	0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs11712061	0.93[ASN][1000 genomes]
rs11714673	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs13061290	0.86[ASN][1000 genomes]
rs2043581	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs34348685	0.92[ASN][1000 genomes]
rs4241526	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4241527	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4350869	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4563353	0.91[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs4566480	0.91[JPT][hapmap]
rs4858616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255443	0.83[AFR][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	nsv834640	chr3:24339779-24493605	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
3	nsv834642	chr3:24475558-24640593	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4858617	NGLY1	cis	parietal	SCAN
rs4858617	PPIL6	trans	brain	seeQTL
rs4858617	CDKL3	trans	brain	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24458800-24490200	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:24477000-24493000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:24477200-24490400	Weak transcription	Aorta	Aorta
4	chr3:24477200-24493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:24478200-24491400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:24478400-24490000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:24478400-24493400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:24482600-24493000	Weak transcription	Right Atrium	heart
9	chr3:24482800-24488200	Weak transcription	Stomach Mucosa	stomach
10	chr3:24483000-24490400	Weak transcription	Left Ventricle	heart
11	chr3:24483000-24490400	Weak transcription	Pancreas	Pancrea
12	chr3:24483000-24490400	Weak transcription	Right Ventricle	heart
13	chr3:24483600-24487800	Weak transcription	Fetal Intestine Large	intestine
14	chr3:24483600-24487800	Weak transcription	K562	blood
15	chr3:24484000-24488800	Weak transcription	Fetal Intestine Small	intestine
16	chr3:24486200-24489600	Weak transcription	Liver	Liver
17	chr3:24486400-24490800	Weak transcription	Psoas Muscle	Psoas
18	chr3:24487200-24488200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:24487200-24488400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr3:24487600-24488000	Enhancers	Breast Myoepithelial Primary Cells	Breast

Quick Search: