Variant report

Variant	rs12124669
Chromosome Location	chr1:212994767-212994768
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212986725..212988338-chr1:212992887..212995652,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1032962	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1032963	0.82[ASN][1000 genomes]
rs10779583	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10864002	0.94[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120028	0.83[ASN][1000 genomes]
rs11120034	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11120038	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11120043	0.82[GIH][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes]
rs12038225	0.91[ASN][1000 genomes]
rs12133194	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12568552	0.87[ASN][1000 genomes]
rs12744555	0.94[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12757944	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs15702	0.88[ASW][hapmap];0.92[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs1813705	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2456827	0.83[ASN][1000 genomes]
rs2884675	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3738800	0.81[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs3949369	0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4951464	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4951639	0.94[ASW][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs6540766	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6540767	0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6681851	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6685864	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6686145	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6689799	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6696870	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6696908	0.89[EUR][1000 genomes]
rs7514070	0.92[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs7528303	0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[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	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	esv2756884	chr1:212925429-213006397	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2758997	chr1:212925429-213006397	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12124669	LQK1	cis	lesional skin	skin_eQTL
rs12124669	LQK1	cis	parietal	SCAN
rs12124669	NEK2	cis	parietal	SCAN
rs12124669	FLVCR1-AS1	cis	Adipose Subcutaneous	GTEx
rs12124669	NCRNA00292	cis	lymphoblastoid	seeQTL
rs12124669	FLVCR1-AS1	cis	Esophagus Muscularis	GTEx
rs12124669	FLVCR1-AS1	cis	lung	GTEx
rs12124669	LOC642946	cis	multi-tissue	Pritchard
rs12124669	FLVCR1-AS1	cis	Whole Blood	GTEx
rs12124669	FLVCR	cis	multi-tissue	Pritchard
rs12124669	C1orf48	cis	multi-tissue	Pritchard
rs12124669	NSL1	cis	lymphoblastoid	seeQTL
rs12124669	LQK1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212966000-212997400	Weak transcription	Aorta	Aorta
2	chr1:212975800-212997800	Weak transcription	Brain Substantia Nigra	brain
3	chr1:212976200-212998800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:212979600-213001000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:212980800-213001000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:212988400-212998800	Weak transcription	Adipose Nuclei	Adipose
7	chr1:212988600-212998400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:212990400-212995600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:212990800-212998600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:212991000-212998800	Weak transcription	Stomach Mucosa	stomach
11	chr1:212992400-212994800	Enhancers	HepG2	liver
12	chr1:212993200-212995000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr1:212994000-212999000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:212994600-212995000	Enhancers	GM12878-XiMat	blood

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