Variant report

Variant	rs7628293
Chromosome Location	chr3:158323665-158323666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12107643	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs12496662	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13074694	0.85[CHB][hapmap]
rs1435642	0.85[CHB][hapmap]
rs1435643	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1595028	0.80[CHB][hapmap]
rs15967	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656376	0.80[CHB][hapmap]
rs1656377	0.85[CHB][hapmap]
rs1714507	0.80[CHB][hapmap]
rs1714518	0.80[CHB][hapmap]
rs17629390	0.84[CHB][hapmap]
rs17630086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1836688	0.85[CHB][hapmap]
rs1864507	0.85[CHB][hapmap]
rs2303909	0.85[CHB][hapmap]
rs2364274	0.85[CHB][hapmap]
rs2731112	0.81[CHB][hapmap]
rs3765025	0.85[CHB][hapmap]
rs3845272	0.80[ASN][1000 genomes]
rs45471897	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4875	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs55875763	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55999561	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62287934	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62289789	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441206	0.80[CHB][hapmap]
rs6772483	0.85[CHB][hapmap]
rs6774829	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6776225	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6780477	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6787486	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6795376	0.80[CHB][hapmap]
rs6800914	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs6803047	0.85[CHB][hapmap]
rs6804259	0.84[CHB][hapmap];0.81[ASN][1000 genomes]
rs73154344	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7612250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7612520	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613824	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7620927	0.80[CHB][hapmap]
rs7621897	0.85[CHB][hapmap]
rs7622451	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7631310	0.85[CHB][hapmap]
rs7647356	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8455	0.85[CHB][hapmap]
rs891464	0.85[CHB][hapmap]
rs959654	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9819567	0.85[CHB][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	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1014381	chr3:158070451-158350118	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	esv2763312	chr3:158193512-158420588	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv877691	chr3:158245883-158359667	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv869644	chr3:158308783-158426343	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7628293	GFM1	cis	cerebellum	SCAN
rs7628293	LXN	cis	cerebellum	SCAN
rs7628293	IQCJ	cis	parietal	SCAN
rs7628293	LXN	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158290400-158324400	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:158299400-158329400	Weak transcription	Left Ventricle	heart
3	chr3:158305600-158330200	Weak transcription	Brain Anterior Caudate	brain
4	chr3:158305800-158328800	Weak transcription	Ovary	ovary
5	chr3:158311400-158329800	Weak transcription	Brain Angular Gyrus	brain
6	chr3:158314200-158324400	Weak transcription	NHDF-Ad	bronchial
7	chr3:158315600-158324600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:158316000-158326400	Weak transcription	Right Ventricle	heart
9	chr3:158316800-158324600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:158318800-158324000	Weak transcription	Adipose Nuclei	Adipose
11	chr3:158318800-158325200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:158320400-158323800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:158320800-158324600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:158321400-158325800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:158321600-158323800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:158322200-158324800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:158322400-158324000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:158322600-158326000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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