Variant report

Variant	rs1978516
Chromosome Location	chr3:21556404-21556405
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	POLR2A	chr3:21556230-21556608	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr3:21556076-21556602	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:21533469..21535837-chr3:21555368..21557096,2	K562	blood:
2	chr3:21534337..21537084-chr3:21554573..21557096,2	K562	blood:
3	chr3:21554662..21556901-chr3:21563061..21566004,2	K562	blood:

Variant related genes	Relation type
ZNF385D	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10510513	0.85[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13317601	0.81[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1457590	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162411	0.81[JPT][hapmap]
rs162412	0.81[JPT][hapmap]
rs1983039	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2059400	0.85[JPT][hapmap]
rs3860577	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3860578	0.81[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs4858329	0.81[JPT][hapmap]
rs6789053	0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs7615120	0.84[JPT][hapmap]
rs7642500	0.81[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]
rs7646837	0.81[CEU][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9310647	0.90[JPT][hapmap]
rs9310648	0.92[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9310649	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs9810352	0.81[JPT][hapmap]
rs9829496	0.81[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862072	0.85[CHD][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs9862207	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006471	chr3:21385627-21596955	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv534005	chr3:21387588-22003293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1000828	chr3:21399870-21565580	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv536515	chr3:21399870-21565580	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1010460	chr3:21516810-21839871	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1978516	TBC1D5	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21515800-21563000	Weak transcription	Fetal Stomach	stomach
2	chr3:21526200-21559000	Weak transcription	Aorta	Aorta
3	chr3:21550000-21561800	Weak transcription	Fetal Brain Male	brain
4	chr3:21553200-21574400	Weak transcription	Fetal Muscle Leg	muscle

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