Variant report

Variant	rs16823238
Chromosome Location	chr1:184440728-184440729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184434578..184437265-chr1:184439841..184442761,2	MCF-7	breast:
2	chr1:184439360..184441984-chr1:184443023..184445236,2	K562	blood:
3	chr1:184440449..184442376-chr1:184450326..184452605,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10399817	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10911610	0.89[CHB][hapmap]
rs12117823	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs12120604	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12121612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12127697	0.94[CHB][hapmap];0.88[GIH][hapmap]
rs12129904	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12138103	0.93[CHB][hapmap];0.94[ASN][1000 genomes]
rs1535132	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16823195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16823197	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs2207526	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2207527	0.95[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs58231072	0.96[ASN][1000 genomes]
rs6659261	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6683932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6693408	0.94[CHB][hapmap];0.88[GIH][hapmap]
rs7513091	0.94[CHB][hapmap];0.88[GIH][hapmap]
rs7525267	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7548188	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16823238	EDEM3	cis	parietal	SCAN
rs16823238	TDRD5	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184425400-184442200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:184427400-184443800	Weak transcription	Esophagus	oesophagus
3	chr1:184427400-184444000	Weak transcription	Lung	lung
4	chr1:184427400-184448400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:184429000-184454800	Weak transcription	Aorta	Aorta
6	chr1:184429400-184449600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:184429600-184442200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:184430600-184444000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:184430600-184449800	Weak transcription	Right Ventricle	heart
10	chr1:184430600-184450000	Weak transcription	Fetal Stomach	stomach
11	chr1:184431400-184446400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:184431800-184447600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:184432000-184443400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr1:184433200-184442200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:184433600-184442000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:184433600-184449600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:184433800-184443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:184436800-184442400	Weak transcription	Left Ventricle	heart
19	chr1:184436800-184442400	Weak transcription	Ovary	ovary
20	chr1:184436800-184444000	Weak transcription	Pancreas	Pancrea
21	chr1:184437000-184441000	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:184438000-184450600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:184439000-184441000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:184439200-184453600	Weak transcription	Fetal Brain Female	brain
25	chr1:184439400-184440800	Weak transcription	Fetal Heart	heart
26	chr1:184439400-184441000	Weak transcription	Fetal Brain Male	brain
27	chr1:184440400-184441000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:184440400-184441200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:184440400-184441600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:184440600-184440800	Enhancers	Fetal Muscle Trunk	muscle
31	chr1:184440600-184441000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:184440600-184441000	Enhancers	Psoas Muscle	Psoas
33	chr1:184440600-184441000	Enhancers	Right Atrium	heart
34	chr1:184440600-184441600	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr1:184440600-184445800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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