Variant report

Variant	rs149956
Chromosome Location	chr6:28036251-28036252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr6:28035828-28036380	HEK293	kidney:	n/a	chr6:28036077-28036087 chr6:28036076-28036085 chr6:28036073-28036089 chr6:28036073-28036089 chr6:28036074-28036088
2	KAP1	chr6:28035728-28036340	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28031578..28034623-chr6:28036187..28038874,3	K562	blood:
2	chr6:28035744..28039366-chr6:28039863..28043405,5	K562	blood:
3	chr6:27975426..27977034-chr6:28033803..28036547,2	K562	blood:

Variant related genes	Relation type
OR1F12	TF binding region
ENSG00000220721	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1150668	0.89[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1150670	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1150679	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1150686	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1150690	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1150694	0.80[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1150705	0.81[JPT][hapmap]
rs1150707	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs1150709	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs1150711	0.81[JPT][hapmap]
rs1150716	0.81[AMR][1000 genomes]
rs12214383	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs1225618	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1225710	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1225715	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1233713	0.92[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs12530158	0.91[JPT][hapmap]
rs13408	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs149963	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs149971	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs149976	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1531681	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs156737	0.86[AFR][1000 genomes]
rs1654774	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1736891	0.92[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs1736895	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs2021826	0.96[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203869	0.96[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs203878	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2142730	0.81[AMR][1000 genomes]
rs2622320	0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap]
rs2622322	0.96[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs276362	1.00[YRI][hapmap]
rs2791333	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7206	0.92[CEU][hapmap];0.81[JPT][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	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs149956	AL022393.7	cis	Nerve Tibial	GTEx
rs149956	ZSCAN23	cis	Artery Tibial	GTEx
rs149956	AL022393.7	cis	Heart Left Ventricle	GTEx
rs149956	AL022393.7	cis	Muscle Skeletal	GTEx
rs149956	ZNF323	cis	Cerebellum	GTEx
rs149956	AL022393.7	cis	Esophagus Muscularis	GTEx
rs149956	AL022393.7	cis	Artery Tibial	GTEx
rs149956	AL022393.7	cis	lung	GTEx
rs149956	ZSCAN31	cis	Thyroid	GTEx
rs149956	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs149956	ZSCAN23	cis	Muscle Skeletal	GTEx
rs149956	ZNF323	cis	Temporal Cortex	GTEx
rs149956	AL022393.7	cis	Artery Aorta	GTEx
rs149956	ZSCAN12	Cis_1M	lymphoblastoid	RTeQTL
rs149956	RP5-874C20.3	cis	Thyroid	GTEx
rs149956	ZNF323	cis	Frontal Cortex	GTEx
rs149956	ZSCAN31	cis	lung	GTEx
rs149956	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs149956	ZSCAN23	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28035800-28037200	Enhancers	K562	blood

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