Variant report

Variant	rs12510869
Chromosome Location	chr4:77024534-77024535
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:77014220..77016956-chr4:77022006..77024608,2	K562	blood:
2	chr4:77024140..77027603-chr4:77067488..77070849,3	K562	blood:
3	chr4:77022675..77026827-chr4:77067488..77070849,4	K562	blood:

Variant related genes	Relation type
ENSG00000138750	Chromatin interaction
ENSG00000265931	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10033843	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs11097237	0.99[ASN][1000 genomes]
rs1127705	0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12499900	0.86[YRI][hapmap]
rs13130116	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13134121	0.91[YRI][hapmap]
rs13136760	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13141802	0.80[ASN][1000 genomes]
rs17001357	0.96[YRI][hapmap]
rs17001409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17001416	0.82[JPT][hapmap];0.89[YRI][hapmap];0.80[ASN][1000 genomes]
rs34978911	0.80[ASN][1000 genomes]
rs35713908	0.80[ASN][1000 genomes]
rs4077787	0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs4241584	0.97[GIH][hapmap]
rs4859422	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859423	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859425	0.92[YRI][hapmap]
rs4859426	0.82[JPT][hapmap];0.82[YRI][hapmap]
rs59050354	0.80[ASN][1000 genomes]
rs66828967	0.81[AFR][1000 genomes]
rs6829592	0.82[YRI][hapmap]
rs6856609	0.82[YRI][hapmap]
rs7673428	0.81[ASN][1000 genomes]
rs7682766	0.92[ASW][hapmap]
rs7689378	0.80[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	nsv529613	chr4:76654941-77081576	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1009047	chr4:76989180-77077885	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12510869	ANKRD56	cis	cerebellum	SCAN
rs12510869	NUP54	cis	parietal	SCAN
rs12510869	THAP6	cis	cerebellum	SCAN
rs12510869	MTHFD2L	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77015200-77025400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:77016400-77025000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr4:77017000-77034400	Weak transcription	Right Ventricle	heart
4	chr4:77021200-77026600	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:77024000-77032200	Weak transcription	Left Ventricle	heart
6	chr4:77024400-77024800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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