Variant report

Variant	rs13221639
Chromosome Location	chr7:108080565-108080566
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108067231..108072750-chr7:108078077..108081806,4	K562	blood:
2	chr7:108069636..108072852-chr7:108078819..108081993,4	MCF-7	breast:
3	chr7:108073988..108076777-chr7:108078660..108081036,2	K562	blood:
4	chr7:108078179..108086501-chr7:108093460..108098271,13	MCF-7	breast:
5	chr7:108076964..108078659-chr7:108079671..108082296,2	K562	blood:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10230518	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10273997	0.89[TSI][hapmap]
rs10278246	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1034825	0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1034829	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11983030	0.80[GIH][hapmap];0.87[MEX][hapmap]
rs12333431	0.87[MEX][hapmap]
rs1859769	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs194585	0.89[TSI][hapmap]
rs2214916	0.80[EUR][1000 genomes]
rs2284290	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2284291	0.84[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2284292	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300043	0.83[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs2300045	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs2300049	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2300050	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2300053	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2396001	0.89[TSI][hapmap]
rs3763462	0.86[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3815252	0.89[TSI][hapmap]
rs40849	0.89[TSI][hapmap]
rs40856	0.89[TSI][hapmap]
rs4730320	0.87[ASN][1000 genomes]
rs6466239	0.89[TSI][hapmap]
rs6976478	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs726471	0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs917251	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13221639	LHFPL3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108067600-108081000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:108067800-108089400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:108068000-108089400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:108069000-108086000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr7:108075200-108085200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:108075400-108081000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:108075400-108081200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr7:108075800-108089400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:108076200-108094800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:108076400-108080800	Weak transcription	A549	lung

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