Variant report

Variant	rs2020862
Chromosome Location	chr1:171168584-171168585
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10798263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10798271	0.89[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs10912537	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10912552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10912593	0.89[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap]
rs11806072	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs12078953	0.95[JPT][hapmap]
rs12080576	0.93[JPT][hapmap]
rs12566823	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.97[MKK][hapmap]
rs17350523	0.95[JPT][hapmap]
rs2064078	0.95[JPT][hapmap]
rs2075987	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2075990	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2075991	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2179105	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2205724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2205729	0.95[JPT][hapmap]
rs2236874	0.95[JPT][hapmap]
rs3738813	0.95[JPT][hapmap]
rs3754495	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap]
rs3768569	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3768570	0.95[JPT][hapmap]
rs6425394	0.95[JPT][hapmap]
rs6657314	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs6692347	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7531971	0.95[JPT][hapmap]
rs926268	0.95[JPT][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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	esv10193	chr1:171128845-171414611	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv831882	chr1:171166224-171326083	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2020862	TNFSF18	cis	cerebellum	SCAN
rs2020862	FMO2	cis	parietal	SCAN
rs2020862	FMO1	cis	cerebellum	SCAN
rs2020862	FMO2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171156600-171169800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr1:171156600-171177200	Weak transcription	Esophagus	oesophagus
3	chr1:171156600-171179600	Weak transcription	NHLF	lung
4	chr1:171156800-171179600	Weak transcription	Right Ventricle	heart
5	chr1:171161000-171171800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:171165400-171168800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:171165600-171173400	Strong transcription	Left Ventricle	heart
8	chr1:171165800-171174400	Weak transcription	Stomach Mucosa	stomach
9	chr1:171166000-171169600	Strong transcription	Aorta	Aorta
10	chr1:171166000-171174600	Weak transcription	Pancreas	Pancrea
11	chr1:171166000-171178000	Weak transcription	Psoas Muscle	Psoas
12	chr1:171166000-171184000	Weak transcription	Gastric	stomach
13	chr1:171166400-171169400	Weak transcription	Right Atrium	heart
14	chr1:171166600-171175400	Strong transcription	Adipose Nuclei	Adipose
15	chr1:171167200-171169400	Weak transcription	Fetal Brain Male	brain
16	chr1:171167200-171187800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr1:171168400-171169200	ZNF genes & repeats	Lung	lung
18	chr1:171168400-171170200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr1:171168400-171170400	Strong transcription	Fetal Lung	lung
20	chr1:171168400-171171800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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