Variant report

Variant	rs16823145
Chromosome Location	chr1:184397915-184397916
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:184393745..184397923-chr1:184400425..184402634,3	MCF-7	breast:
2	chr1:184392135..184393855-chr1:184396238..184398930,2	K562	blood:
3	chr1:184397306..184399286-chr1:184405791..184407775,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10489723	0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16823065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16823118	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs16823340	0.85[TSI][hapmap]
rs16823344	0.85[TSI][hapmap]
rs17255321	0.88[MEX][hapmap]
rs2207521	0.88[MEX][hapmap]
rs2207524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2378842	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3814334	1.00[CHB][hapmap]
rs57336256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58863963	0.88[ASN][1000 genomes]
rs59158738	0.88[ASN][1000 genomes]
rs59237100	0.88[ASN][1000 genomes]
rs60066136	0.88[ASN][1000 genomes]
rs6424951	0.96[ASN][1000 genomes]
rs6695258	1.00[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6698504	1.00[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73061677	0.88[ASN][1000 genomes]
rs73061691	0.88[ASN][1000 genomes]
rs73063504	0.88[ASN][1000 genomes]
rs73063508	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73063512	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73063527	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525041	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7540074	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7550032	0.88[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs16823145	TTR	trans	brain	seeQTL
rs16823145	SCGN	trans	brain	seeQTL
rs16823145	SH2D2A	trans	brain	seeQTL
rs16823145	CHRNA3	trans	brain	seeQTL
rs16823145	PENK	trans	brain	seeQTL
rs16823145	GUCA1C	trans	brain	seeQTL
rs16823145	SLC5A7	trans	brain	seeQTL
rs16823145	LRTM1	trans	brain	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184378200-184402400	Weak transcription	Fetal Lung	lung
2	chr1:184383800-184412400	Weak transcription	Fetal Stomach	stomach
3	chr1:184387000-184400200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:184387200-184403400	Weak transcription	Aorta	Aorta
5	chr1:184388000-184400000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:184389200-184399800	Weak transcription	A549	lung
7	chr1:184389400-184399400	Weak transcription	NHLF	lung
8	chr1:184390600-184401600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:184390600-184422400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:184391400-184398000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:184392200-184408200	Weak transcription	Esophagus	oesophagus
12	chr1:184392400-184398200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr1:184394600-184398600	Weak transcription	HMEC	breast
14	chr1:184394800-184398000	Weak transcription	Lung	lung
15	chr1:184395000-184402200	Weak transcription	Pancreas	Pancrea
16	chr1:184395000-184405600	Weak transcription	Fetal Intestine Small	intestine
17	chr1:184395200-184405000	Weak transcription	Fetal Intestine Large	intestine
18	chr1:184395400-184408000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:184395600-184398000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:184395600-184398000	Weak transcription	Small Intestine	intestine
21	chr1:184395800-184398000	Weak transcription	Fetal Heart	heart
22	chr1:184395800-184405600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:184396000-184412800	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:184396200-184402400	Weak transcription	Stomach Mucosa	stomach
25	chr1:184396200-184412800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:184396200-184418800	Weak transcription	NHEK	skin
27	chr1:184396200-184419000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:184396400-184402200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:184396400-184430000	Weak transcription	Spleen	Spleen
30	chr1:184396800-184398800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:184396800-184404800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:184397000-184402200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr1:184397000-184402200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:184397200-184398000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:184397200-184402200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:184397600-184398200	Enhancers	Psoas Muscle	Psoas
37	chr1:184397800-184398200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:184397800-184398400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:184397800-184398400	Enhancers	Left Ventricle	heart
40	chr1:184397800-184398400	Genic enhancers	Rectal Mucosa Donor 31	rectum
41	chr1:184397800-184398400	Enhancers	Right Ventricle	heart
42	chr1:184397800-184398400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
43	chr1:184397800-184398600	Enhancers	Right Atrium	heart

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