Variant report

Variant	rs429252
Chromosome Location	chr7:107745554-107745555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:107744231..107746963-chr7:107748400..107751229,2	MCF-7	breast:
2	chr7:107743149..107746121-chr7:107770515..107772885,2	K562	blood:

Variant related genes	Relation type
ENSG00000091128	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs17155006	0.92[CEU][hapmap]
rs1735499	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs366690	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs367538	0.88[CEU][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs369505	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs369508	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs370495	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs371024	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs377007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs377661	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs378334	0.92[EUR][1000 genomes]
rs378641	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs378962	0.92[ASW][hapmap];0.84[CEU][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs379821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs380046	0.81[EUR][1000 genomes]
rs382131	0.81[EUR][1000 genomes]
rs387981	0.87[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs389486	0.81[EUR][1000 genomes]
rs397941	0.81[EUR][1000 genomes]
rs399290	0.80[EUR][1000 genomes]
rs399882	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs401066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs401145	0.80[EUR][1000 genomes]
rs401487	0.84[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs402113	0.92[ASW][hapmap];0.84[CEU][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs402264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403731	0.85[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405239	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs405869	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs409815	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410866	0.84[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs411396	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413412	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs416811	0.81[EUR][1000 genomes]
rs418255	0.81[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs419031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs420753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424866	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs424978	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs425623	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs426812	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs430995	0.88[CEU][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs433534	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs435125	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435361	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs435522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435744	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436573	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs437336	0.81[EUR][1000 genomes]
rs440938	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs445661	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs445662	0.86[EUR][1000 genomes]
rs446566	0.81[CEU][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs446800	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448342	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs448559	0.92[ASW][hapmap];0.84[CEU][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs448742	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs448833	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs450722	0.81[EUR][1000 genomes]
rs451252	0.92[ASW][hapmap];0.81[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6974722	0.92[ASW][hapmap];0.84[CEU][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs93619	0.81[EUR][1000 genomes]
rs94604	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs985152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv831089	chr7:107687618-107877240	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs429252	COG5	cis	cerebellum	SCAN
rs429252	DOCK4	cis	cerebellum	SCAN
rs429252	LHFPL3	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107736200-107753400	Weak transcription	Right Atrium	heart
2	chr7:107736400-107756400	Weak transcription	Pancreas	Pancrea
3	chr7:107736600-107747400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:107741000-107748000	Weak transcription	Small Intestine	intestine
5	chr7:107743200-107745600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:107743200-107745600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr7:107743600-107747600	Weak transcription	Fetal Intestine Small	intestine
8	chr7:107743800-107745600	Enhancers	Fetal Stomach	stomach
9	chr7:107744600-107745600	Enhancers	Fetal Muscle Leg	muscle
10	chr7:107745000-107745600	Enhancers	K562	blood
11	chr7:107745000-107747400	Weak transcription	NHLF	lung
12	chr7:107745000-107748600	Weak transcription	A549	lung
13	chr7:107745000-107762600	Weak transcription	Fetal Lung	lung
14	chr7:107745200-107747200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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