Variant report

Variant	rs6664672
Chromosome Location	chr1:62711941-62711942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1050334	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10789108	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs10889309	0.84[ASN][1000 genomes]
rs10889310	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10889313	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10889315	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11207941	0.86[ASN][1000 genomes]
rs11207943	0.87[ASN][1000 genomes]
rs11207944	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11207945	0.91[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11207946	0.87[ASN][1000 genomes]
rs12089897	0.84[ASN][1000 genomes]
rs12120789	0.86[ASN][1000 genomes]
rs12138777	0.82[ASN][1000 genomes]
rs12144282	0.86[ASN][1000 genomes]
rs2067994	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2457812	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481689	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2666478	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2774928	0.84[ASN][1000 genomes]
rs41289438	0.86[ASN][1000 genomes]
rs4322258	0.84[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap]
rs61775734	0.86[ASN][1000 genomes]
rs61775736	0.86[ASN][1000 genomes]
rs61775737	0.86[ASN][1000 genomes]
rs6660963	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6680953	0.86[ASN][1000 genomes]
rs6688986	0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6696307	0.87[ASN][1000 genomes]
rs6696486	0.86[ASN][1000 genomes]
rs7553446	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6664672	JUN	cis	cerebellum	SCAN
rs6664672	OR4K2	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62704000-62720600	Weak transcription	Right Atrium	heart
2	chr1:62704200-62712000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:62704400-62713200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:62706400-62713200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:62707600-62719600	Weak transcription	Fetal Kidney	kidney
6	chr1:62707600-62732000	Weak transcription	Gastric	stomach
7	chr1:62707800-62712000	Weak transcription	Colonic Mucosa	Colon
8	chr1:62707800-62713200	Weak transcription	Fetal Brain Female	brain
9	chr1:62707800-62727400	Weak transcription	Pancreas	Pancrea
10	chr1:62708000-62713000	Weak transcription	Fetal Heart	heart
11	chr1:62708200-62720000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:62710000-62712000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:62710400-62712000	Strong transcription	Placenta	Placenta
14	chr1:62710400-62713600	Strong transcription	Fetal Stomach	stomach
15	chr1:62710600-62713800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr1:62710600-62713800	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:62710800-62712000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:62710800-62731800	Weak transcription	Fetal Intestine Small	intestine
19	chr1:62711400-62712000	Strong transcription	Fetal Lung	lung
20	chr1:62711400-62712200	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr1:62711400-62718000	Weak transcription	HepG2	liver
22	chr1:62711600-62730600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:62711800-62712000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:62711800-62712000	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr1:62711800-62713400	Weak transcription	Adipose Nuclei	Adipose

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