Variant report

Variant	rs149976
Chromosome Location	chr6:27987776-27987777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27862119..27863751-chr6:27985739..27988180,2	K562	blood:
2	chr6:27958100..27959630-chr6:27985165..27988102,2	K562	blood:
3	chr6:27981949..27984584-chr6:27987627..27989149,2	MCF-7	breast:
4	chr6:27985193..27988547-chr6:27998544..28000332,3	K562	blood:
5	chr6:27979427..27983330-chr6:27984684..27988403,5	K562	blood:
6	chr6:27982740..27985461-chr6:27987280..27989887,2	K562	blood:

Variant related genes	Relation type
ENSG00000199851	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1150668	0.88[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs1150694	0.90[JPT][hapmap]
rs1225618	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap]
rs1225710	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes]
rs1225715	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap]
rs12530158	0.91[JPT][hapmap]
rs149956	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]
rs149963	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs149971	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs156735	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs156737	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1654774	0.81[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap]
rs1736891	1.00[ASW][hapmap];0.92[CEU][hapmap];0.80[JPT][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.82[AFR][1000 genomes]
rs2021826	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs203869	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs203878	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap]
rs2622320	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs2622322	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AFR][1000 genomes]
rs276362	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs276369	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs276371	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2791333	0.90[ASW][hapmap];0.96[CEU][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	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
4	nsv883513	chr6:27982152-28033087	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv1817841	chr6:27984907-28007435	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv981052	chr6:27987196-28024382	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:28)

SNP	Gene	Cis/trans	Tissue	Source
rs149976	ZSCAN23	cis	parietal	SCAN
rs149976	AL022393.7	cis	Esophagus Muscularis	GTEx
rs149976	ZSCAN31	cis	Esophagus Muscularis	GTEx
rs149976	ZNF323	cis	Frontal Cortex	GTEx
rs149976	ZSCAN23	cis	Adipose Subcutaneous	GTEx
rs149976	ZNF323	cis	Temporal Cortex	GTEx
rs149976	ZNF323	cis	cerebellum	SCAN
rs149976	ZNF323	cis	parietal	SCAN
rs149976	AL022393.7	cis	lung	GTEx
rs149976	ZKSCAN3	cis	parietal	SCAN
rs149976	ZNF187	cis	cerebellum	SCAN
rs149976	AL022393.7	cis	Artery Aorta	GTEx
rs149976	ZKSCAN3	cis	cerebellum	SCAN
rs149976	AL022393.7	cis	Nerve Tibial	GTEx
rs149976	RP5-874C20.3	cis	Thyroid	GTEx
rs149976	ZSCAN23	cis	Muscle Skeletal	GTEx
rs149976	ZSCAN23	cis	Artery Tibial	GTEx
rs149976	AL022393.7	cis	Heart Left Ventricle	GTEx
rs149976	NKAPL	cis	parietal	SCAN
rs149976	ZSCAN23	cis	cerebellum	SCAN
rs149976	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs149976	ZSCAN31	cis	lung	GTEx
rs149976	ZNF323	cis	brain	seeQTL
rs149976	ZNF192	cis	cerebellum	SCAN
rs149976	AL022393.7	cis	Muscle Skeletal	GTEx
rs149976	AL022393.7	cis	Artery Tibial	GTEx
rs149976	ZSCAN31	cis	Thyroid	GTEx
rs149976	ZNF323	cis	Cerebellum	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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