Variant report

Variant	rs4676787
Chromosome Location	chr3:120194175-120194176
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11710885	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11712887	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259310	0.84[ASN][1000 genomes]
rs13099637	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[ASN][1000 genomes]
rs35547467	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4676789	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61797572	0.84[AFR][1000 genomes]
rs61797573	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7622005	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838077	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4676787	NR1I2	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120186000-120195000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr3:120186600-120195000	Enhancers	Placenta	Placenta
3	chr3:120189200-120194600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:120189200-120194800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:120190000-120196200	Weak transcription	Left Ventricle	heart
6	chr3:120190200-120194600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:120191200-120194600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:120191800-120195600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:120192200-120195200	Enhancers	HSMMtube	muscle
10	chr3:120192800-120194800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:120192800-120195600	Weak transcription	Fetal Heart	heart
12	chr3:120193000-120194200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:120193200-120195000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:120193200-120195400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:120193400-120194600	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:120193400-120195000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:120193400-120195000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr3:120193400-120195200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:120193400-120195400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr3:120193400-120195400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr3:120193600-120194600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:120193600-120194800	Weak transcription	NH-A	brain
23	chr3:120193600-120196800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr3:120193800-120194800	Weak transcription	NHDF-Ad	bronchial
25	chr3:120193800-120205800	Weak transcription	HSMM	muscle
26	chr3:120194000-120194600	Weak transcription	Osteobl	bone
27	chr3:120194000-120195000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:120194000-120196400	Enhancers	Stomach Smooth Muscle	stomach

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