Variant report

Variant	rs1523599
Chromosome Location	chr3:135686355-135686356
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs12630389	0.98[ASN][1000 genomes]
rs12632791	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12633805	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12637541	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059064	0.83[ASN][1000 genomes]
rs13065499	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13069408	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072433	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072690	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13072782	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13075579	0.92[ASN][1000 genomes]
rs13078865	0.88[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs13084404	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13092707	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13097172	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs13097176	0.81[ASN][1000 genomes]
rs13097267	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1523593	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1523598	0.88[ASN][1000 genomes]
rs1523600	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16843560	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16843611	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2140450	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2177407	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2400649	0.83[ASN][1000 genomes]
rs34447526	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35097316	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35209948	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35532770	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35946332	0.83[ASN][1000 genomes]
rs35961065	0.87[ASN][1000 genomes]
rs3946444	0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs4075999	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4331626	0.82[ASN][1000 genomes]
rs4678224	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4678288	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4678432	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4678434	0.88[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4678435	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55873361	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56152207	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57594457	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60070757	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61791712	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61791714	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6439603	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439605	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6439609	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6439610	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6439614	0.82[ASN][1000 genomes]
rs6439615	0.83[ASN][1000 genomes]
rs6439618	0.83[ASN][1000 genomes]
rs6439622	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6439623	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6439624	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6771950	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6775261	0.83[ASN][1000 genomes]
rs6779903	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6793273	0.82[ASN][1000 genomes]
rs6803786	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7433592	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7610302	0.83[ASN][1000 genomes]
rs7625177	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7625607	0.85[ASN][1000 genomes]
rs7635621	0.83[ASN][1000 genomes]
rs7650079	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9289501	0.87[ASN][1000 genomes]
rs940229	0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9682712	0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9758578	0.91[ASN][1000 genomes]
rs9846554	0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9852009	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9852169	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9856799	0.94[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs9866235	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap]
rs9868239	0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460860	chr3:135107678-135769006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv591829	chr3:135107678-135769006	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv829732	chr3:135561706-135756840	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	esv3374702	chr3:135649303-135686527	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1523599	TMEM22	cis	cerebellum	SCAN
rs1523599	RBP2	cis	cerebellum	SCAN
rs1523599	SLC9A7	trans	cerebellum	SCAN
rs1523599	NCK1	cis	parietal	SCAN
rs1523599	MSL2	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135683800-135687200	Active TSS	Stomach Smooth Muscle	stomach
2	chr3:135684000-135686400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:135684000-135686400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:135684000-135686400	Active TSS	NHLF	lung
5	chr3:135684000-135686600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:135684000-135686600	Active TSS	Right Ventricle	heart
7	chr3:135684000-135687000	Active TSS	Right Atrium	heart
8	chr3:135684200-135686400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:135684200-135686800	Active TSS	Aorta	Aorta
10	chr3:135685400-135686400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:135685400-135686400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:135685400-135692600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:135685600-135686400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:135685600-135686400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:135685600-135686400	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr3:135685600-135686600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:135685600-135686600	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr3:135685600-135686800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
19	chr3:135685600-135687000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:135685600-135687000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:135685600-135687200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:135685600-135693800	Weak transcription	Gastric	stomach
23	chr3:135685800-135686400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:135685800-135686400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:135685800-135686400	Enhancers	Liver	Liver
26	chr3:135685800-135686400	Flanking Active TSS	Fetal Heart	heart
27	chr3:135685800-135686400	Weak transcription	Psoas Muscle	Psoas
28	chr3:135685800-135686600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr3:135685800-135686600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:135685800-135686800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr3:135685800-135686800	Enhancers	Placenta	Placenta
32	chr3:135685800-135686800	Weak transcription	Left Ventricle	heart
33	chr3:135685800-135687000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:135685800-135687000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:135685800-135687000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr3:135685800-135687000	Enhancers	Fetal Intestine Large	intestine
37	chr3:135685800-135687000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr3:135685800-135687400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr3:135685800-135687400	Enhancers	Brain Angular Gyrus	brain
40	chr3:135685800-135687600	Enhancers	Stomach Mucosa	stomach
41	chr3:135685800-135688400	Weak transcription	Small Intestine	intestine
42	chr3:135685800-135693800	Weak transcription	Lung	lung
43	chr3:135686000-135686400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr3:135686000-135686400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:135686000-135686400	Enhancers	Adipose Nuclei	Adipose
46	chr3:135686000-135686400	Enhancers	Brain Anterior Caudate	brain
47	chr3:135686000-135686400	Enhancers	Brain Substantia Nigra	brain
48	chr3:135686000-135686400	Weak transcription	Pancreas	Pancrea
49	chr3:135686000-135686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr3:135686000-135686400	Active TSS	HMEC	breast

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