Variant report

Variant	rs2102541
Chromosome Location	chr4:120115379-120115380
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-455G16.1.1-3	chr4:120114843-120115546	NONHSAT098035

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11935130	0.81[CHD][hapmap];0.81[GIH][hapmap]
rs11946597	0.81[CEU][hapmap]
rs12642637	0.91[ASN][1000 genomes]
rs12644226	0.93[ASN][1000 genomes]
rs12644283	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12645079	0.86[CHD][hapmap];0.84[GIH][hapmap];0.85[MKK][hapmap]
rs12645965	0.86[CHD][hapmap];0.84[GIH][hapmap];0.85[MKK][hapmap]
rs17049968	0.86[CHD][hapmap];0.83[GIH][hapmap];0.85[MKK][hapmap]
rs1858285	0.81[CHD][hapmap]
rs4833611	0.81[CEU][hapmap]
rs4834761	0.98[ASN][1000 genomes]
rs4834762	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4834769	1.00[YRI][hapmap]
rs55724227	0.83[ASN][1000 genomes]
rs55732167	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55890361	0.96[ASN][1000 genomes]
rs56034803	0.98[ASN][1000 genomes]
rs56083532	0.96[ASN][1000 genomes]
rs57070054	0.91[ASN][1000 genomes]
rs62326299	0.83[ASN][1000 genomes]
rs62326301	0.91[ASN][1000 genomes]
rs62326319	0.91[ASN][1000 genomes]
rs62326320	0.91[ASN][1000 genomes]
rs62326341	0.98[ASN][1000 genomes]
rs62326342	0.98[ASN][1000 genomes]
rs62326344	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326345	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326346	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326347	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326348	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326349	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62326352	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62328369	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72910519	0.91[ASN][1000 genomes]
rs7694500	0.83[ASN][1000 genomes]
rs7694555	0.83[ASN][1000 genomes]
rs8180225	0.82[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv948802	chr4:119844269-120208926	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv1008115	chr4:120007913-120143849	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
4	nsv522386	chr4:120009147-120115379	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2102541	FABP2	cis	Whole Blood	GTEx
rs2102541	FABP2	cis	Heart Left Ventricle	GTEx
rs2102541	FABP2	cis	cerebellum	SCAN
rs2102541	QRFPR	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120101000-120132400	Weak transcription	Left Ventricle	heart
2	chr4:120106200-120119200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:120112200-120116400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:120113000-120125200	Weak transcription	Right Atrium	heart

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