Variant report

Variant	rs7286648
Chromosome Location	chr22:31539614-31539615
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:31534039..31536501-chr22:31538813..31541013,2	K562	blood:
2	chr22:31490963..31492744-chr22:31538317..31540744,2	MCF-7	breast:
3	chr22:31538424..31540248-chr22:31554782..31556431,2	MCF-7	breast:
4	chr22:31537984..31540671-chr22:31548834..31552374,3	K562	blood:
5	chr22:31518708..31521060-chr22:31538019..31540317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138942	Chromatin interaction
ENSG00000185133	Chromatin interaction
ENSG00000264141	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11703927	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12166373	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap]
rs13057841	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs131209	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs140074	0.96[CEU][hapmap];0.82[CHB][hapmap]
rs2027982	0.91[MEX][hapmap]
rs28715	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs34873968	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4820961	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs5994376	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[ASN][1000 genomes]
rs5997887	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5997898	0.87[MEX][hapmap]
rs5997900	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5997909	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5997919	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs5997929	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap]
rs6518737	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs713947	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs7285171	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.83[EUR][1000 genomes]
rs7287402	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap]
rs7288735	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs739427	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap]
rs8141987	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8143002	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9619169	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9621216	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9621221	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][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	nsv829173	chr22:31450043-31543956	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv914976	chr22:31475307-31543260	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7286648	LIMK2	cis	cerebellum	SCAN
rs7286648	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs7286648	SFI1	cis	cerebellum	SCAN
rs7286648	MN1	cis	parietal	SCAN
rs7286648	CRYBB1	cis	cerebellum	SCAN
rs7286648	SFI1	cis	Thyroid	GTEx
rs7286648	PISD	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31536200-31540800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr22:31536600-31539800	Enhancers	Esophagus	oesophagus
3	chr22:31536600-31540600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr22:31537400-31540000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr22:31538200-31540800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr22:31538600-31540400	Enhancers	NHEK	skin
7	chr22:31538800-31539800	Enhancers	Brain Anterior Caudate	brain
8	chr22:31538800-31539800	Enhancers	Brain Cingulate Gyrus	brain
9	chr22:31538800-31539800	Enhancers	Fetal Muscle Leg	muscle
10	chr22:31538800-31539800	Enhancers	Right Ventricle	heart
11	chr22:31538800-31539800	Enhancers	Spleen	Spleen
12	chr22:31538800-31540000	Enhancers	Brain Hippocampus Middle	brain
13	chr22:31538800-31540000	Enhancers	Brain Substantia Nigra	brain
14	chr22:31538800-31540000	Enhancers	Placenta	Placenta
15	chr22:31538800-31540000	Weak transcription	HMEC	breast
16	chr22:31539000-31540000	Enhancers	Fetal Muscle Trunk	muscle
17	chr22:31539400-31539800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr22:31539400-31540000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr22:31539600-31539800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr22:31539600-31543800	Weak transcription	Right Atrium	heart
21	chr22:31539600-31544800	Weak transcription	Brain Inferior Temporal Lobe	brain

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