Variant report

Variant	rs726471
Chromosome Location	chr7:108102346-108102347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108094254..108096481-chr7:108100316..108102970,2	K562	blood:
2	chr7:108102278..108104184-chr7:108111480..108113045,2	MCF-7	breast:
3	chr7:108101662..108103769-chr7:108105980..108107741,2	MCF-7	breast:
4	chr7:108092620..108097023-chr7:108100316..108104112,6	K562	blood:
5	chr7:108095530..108098596-chr7:108100575..108103691,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10225561	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs10230518	0.90[JPT][hapmap]
rs10273997	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10278246	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1034825	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs1034829	0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13221639	0.81[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs13244602	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1473131	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17339110	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1859769	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1859771	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1859772	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1859773	0.83[CHB][hapmap]
rs1859774	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1859775	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs194585	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs194586	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2214916	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2284290	0.85[GIH][hapmap]
rs2284291	0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2284292	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2300053	0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2396001	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3763462	1.00[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3815252	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs40846	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40848	0.82[CHD][hapmap]
rs40849	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40856	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs40890	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40892	0.83[CHB][hapmap]
rs40903	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6466239	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6466240	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6966431	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6976478	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73426110	0.93[EUR][1000 genomes]
rs7800334	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7806223	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs917251	0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9640707	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9785006	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs726471	LHFPL3	cis	parietal	SCAN
rs726471	C7orf66	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108097200-108118000	Weak transcription	Aorta	Aorta
2	chr7:108097800-108103200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr7:108100000-108102800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr7:108100400-108103000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:108100400-108106600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr7:108100800-108102800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr7:108100800-108103200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr7:108100800-108108800	Weak transcription	HUVEC	blood vessel
10	chr7:108101000-108103200	Weak transcription	Primary T cells from cord blood	blood
11	chr7:108101000-108119200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:108101200-108102400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:108101400-108102800	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr7:108101400-108116800	Weak transcription	Osteobl	bone
15	chr7:108101600-108102400	Enhancers	Pancreas	Pancrea
16	chr7:108101800-108102600	Enhancers	Fetal Muscle Leg	muscle
17	chr7:108101800-108108400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:108102200-108102400	Enhancers	Brain Hippocampus Middle	brain
19	chr7:108102200-108102400	Enhancers	NH-A	brain
20	chr7:108102200-108102600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:108102200-108102600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:108102200-108102600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:108102200-108102800	Enhancers	Adipose Nuclei	Adipose
24	chr7:108102200-108102800	Enhancers	HSMM	muscle
25	chr7:108102200-108106800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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