Variant report

Variant	rs1661410
Chromosome Location	chr11:101778710-101778711
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	GATA3	chr11:101778585-101778767	SH-SY5Y	brain:	n/a	chr11:101778679-101778686

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:101778672..101780240-chr11:101784628..101787052,2	K562	blood:

Variant related genes	Relation type
ANGPTL5	TF binding region
ENSG00000110318	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1004352	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10791545	0.92[CEU][hapmap];0.87[CHB][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10895220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10895228	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10895231	0.87[CHB][hapmap]
rs11225049	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11225080	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11225093	0.87[CHB][hapmap]
rs12281520	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12787877	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12802591	0.87[CHB][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs1372414	0.87[CHB][hapmap];0.83[GIH][hapmap]
rs1441929	0.87[CHB][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap]
rs1661409	0.90[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1661411	0.87[CHB][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs1783740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119734	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2282612	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59927719	0.92[ASN][1000 genomes]
rs6590941	0.87[CHB][hapmap]
rs7105709	0.84[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs7107662	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7122772	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs975810	0.87[CHB][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052159	chr11:101439655-101853293	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1051457	chr11:101446705-101837650	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv832250	chr11:101617934-101804020	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3362945	chr11:101736547-102114246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1661410	KIAA1377	cis	parietal	SCAN
rs1661410	MMP7	cis	parietal	SCAN
rs1661410	KIAA1377	cis	cerebellum	SCAN
rs1661410	C11orf70	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101776000-101781600	Weak transcription	Aorta	Aorta
2	chr11:101777200-101778800	Active TSS	Ovary	ovary
3	chr11:101777400-101779800	Weak transcription	NHDF-Ad	bronchial
4	chr11:101778200-101779200	Enhancers	Osteobl	bone
5	chr11:101778400-101778800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:101778400-101779200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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