Variant report

Variant	rs401487
Chromosome Location	chr7:107743409-107743410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107741696..107745542-chr7:107745790..107752287,8	K562	blood:
2	chr7:107736265..107740487-chr7:107741777..107745446,6	K562	blood:
3	chr7:107737719..107739319-chr7:107743143..107745018,2	MCF-7	breast:
4	chr7:107743149..107746121-chr7:107770515..107772885,2	K562	blood:

Variant related genes	Relation type
ENSG00000091128	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1735499	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs366690	0.93[EUR][1000 genomes]
rs367538	0.88[ASW][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs369505	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs369508	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs370495	0.93[EUR][1000 genomes]
rs370533	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs371024	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs376552	0.81[AFR][1000 genomes]
rs377007	0.84[CEU][hapmap];0.91[EUR][1000 genomes]
rs377661	0.91[EUR][1000 genomes]
rs378334	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs378641	0.88[ASW][hapmap];0.86[LWK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs378962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs379821	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs380046	0.94[AFR][1000 genomes]
rs387981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389486	0.92[AFR][1000 genomes]
rs397941	0.92[AFR][1000 genomes]
rs399290	0.84[EUR][1000 genomes]
rs399882	0.89[EUR][1000 genomes]
rs401066	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs401145	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs402113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs402264	0.84[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs403731	0.92[CEU][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs405239	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs405869	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs409815	0.92[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs410286	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs410866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs411396	0.95[EUR][1000 genomes]
rs413412	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs416811	0.85[EUR][1000 genomes]
rs418255	0.81[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs419031	0.84[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs420753	0.84[CEU][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs424866	0.84[EUR][1000 genomes]
rs424978	0.86[YRI][hapmap];0.85[AFR][1000 genomes]
rs425623	0.93[EUR][1000 genomes]
rs429252	0.84[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs430995	0.88[ASW][hapmap];0.97[LWK][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs433534	0.89[TSI][hapmap];0.83[YRI][hapmap]
rs435125	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs435361	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs435522	0.84[CEU][hapmap];0.93[EUR][1000 genomes]
rs435744	0.93[EUR][1000 genomes]
rs436573	0.96[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs437336	0.94[AFR][1000 genomes]
rs440938	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445661	0.91[EUR][1000 genomes]
rs446566	0.81[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs446800	0.93[EUR][1000 genomes]
rs448342	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs448559	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs448742	0.88[ASW][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs448833	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs450722	0.90[AFR][1000 genomes]
rs451252	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730287	0.82[CHB][hapmap]
rs6974722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs94604	0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs985152	0.84[CEU][hapmap];0.93[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs401487	LHFPL3	cis	parietal	SCAN
rs401487	DOCK4	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107736200-107744600	Weak transcription	Fetal Muscle Leg	muscle
2	chr7:107736200-107753400	Weak transcription	Right Atrium	heart
3	chr7:107736400-107744200	Weak transcription	Osteobl	bone
4	chr7:107736400-107756400	Weak transcription	Pancreas	Pancrea
5	chr7:107736600-107747400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr7:107737000-107744600	Weak transcription	Fetal Lung	lung
7	chr7:107739200-107744200	Weak transcription	A549	lung
8	chr7:107740600-107743800	Weak transcription	Fetal Stomach	stomach
9	chr7:107741000-107744400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:107741000-107748000	Weak transcription	Small Intestine	intestine
11	chr7:107741200-107743600	Weak transcription	NHLF	lung
12	chr7:107741200-107744000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:107741800-107744000	Weak transcription	NHDF-Ad	bronchial
14	chr7:107742400-107745000	Enhancers	HepG2	liver
15	chr7:107743200-107743600	Enhancers	Fetal Intestine Small	intestine
16	chr7:107743200-107744000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:107743200-107745000	Flanking Active TSS	K562	blood
18	chr7:107743200-107745200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:107743200-107745200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:107743200-107745200	Enhancers	Placenta	Placenta
21	chr7:107743200-107745600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:107743200-107745600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr7:107743400-107743800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr7:107743400-107744400	Enhancers	Placenta Amnion	Placenta Amnion
25	chr7:107743400-107745000	Enhancers	Fetal Muscle Trunk	muscle
26	chr7:107743400-107745200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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