Variant report

Variant	rs1566823
Chromosome Location	chr2:128018192-128018193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10209678	0.95[ASN][1000 genomes]
rs10803585	0.86[ASN][1000 genomes]
rs10928761	0.89[CHB][hapmap];0.89[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11886231	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11890187	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12052483	0.85[ASN][1000 genomes]
rs12463451	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12465955	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12477214	0.84[ASN][1000 genomes]
rs12479003	0.87[ASN][1000 genomes]
rs12622436	0.86[ASW][hapmap];0.80[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12623948	0.96[ASN][1000 genomes]
rs12692064	0.95[ASN][1000 genomes]
rs12989081	0.84[ASN][1000 genomes]
rs12989154	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12991768	0.82[ASN][1000 genomes]
rs13029237	0.83[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17015199	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1799808	0.80[ASW][hapmap]
rs1850689	0.84[ASN][1000 genomes]
rs2090574	0.86[ASN][1000 genomes]
rs2174270	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2276583	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2896980	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3088374	0.81[MEX][hapmap]
rs34832797	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35293119	0.85[ASN][1000 genomes]
rs35328149	0.96[ASN][1000 genomes]
rs3768866	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150407	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.96[ASN][1000 genomes]
rs4150441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4150454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4150477	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4150495	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4150496	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4233583	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233584	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4497825	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.93[ASN][1000 genomes]
rs4662575	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4662578	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4662580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4662711	0.93[ASN][1000 genomes]
rs4662712	0.84[ASN][1000 genomes]
rs4662717	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4662722	0.96[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4662725	0.85[ASN][1000 genomes]
rs55905117	0.99[ASN][1000 genomes]
rs55998967	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58475809	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59566504	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62157549	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62157555	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6430935	0.97[ASN][1000 genomes]
rs6710535	0.86[ASW][hapmap]
rs6712213	0.96[ASN][1000 genomes]
rs6712446	0.96[ASN][1000 genomes]
rs6712551	0.96[ASN][1000 genomes]
rs6731176	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs6732279	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6754999	0.86[ASW][hapmap]
rs6761447	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71414745	0.90[ASN][1000 genomes]
rs7568261	0.87[ASN][1000 genomes]
rs7580658	0.86[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap]
rs7589451	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs867304	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9636237	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9789510	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]

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	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription 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 target site	8 gene(s)	inside rSNPs	diseases
5	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1566823	ERCC3	cis	parietal	SCAN
rs1566823	ERCC3	cis	Skin Sun Exposed Lower leg	GTEx
rs1566823	ERCC3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128012400-128028000	Weak transcription	Hela-S3	cervix
2	chr2:128012600-128026200	Weak transcription	Stomach Mucosa	stomach
3	chr2:128012800-128019600	Strong transcription	GM12878-XiMat	blood
4	chr2:128012800-128020800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:128013000-128020200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:128013000-128020600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:128013000-128020600	Strong transcription	Fetal Brain Female	brain
8	chr2:128013000-128020600	Strong transcription	Dnd41	blood
9	chr2:128013000-128020800	Strong transcription	Fetal Intestine Large	intestine
10	chr2:128013000-128021200	Strong transcription	Primary T cells from cord blood	blood
11	chr2:128013000-128021800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:128013200-128018400	Weak transcription	Psoas Muscle	Psoas
13	chr2:128013200-128019000	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr2:128013200-128019000	Strong transcription	Ovary	ovary
15	chr2:128013200-128020400	Strong transcription	HepG2	liver
16	chr2:128013200-128020600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:128013200-128020800	Strong transcription	Primary hematopoietic stem cells	blood
18	chr2:128013400-128018800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:128013400-128018800	Strong transcription	Gastric	stomach
20	chr2:128013400-128018800	Strong transcription	Right Ventricle	heart
21	chr2:128013400-128018800	Strong transcription	Spleen	Spleen
22	chr2:128013400-128019000	Strong transcription	Adipose Nuclei	Adipose
23	chr2:128013400-128019000	Strong transcription	Aorta	Aorta
24	chr2:128013400-128019000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:128013400-128019200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:128013400-128019400	Strong transcription	Fetal Stomach	stomach
27	chr2:128013400-128019600	Strong transcription	Placenta	Placenta
28	chr2:128013400-128020000	Strong transcription	Lung	lung
29	chr2:128013400-128020200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:128013400-128020200	Strong transcription	Fetal Intestine Small	intestine
31	chr2:128013400-128020200	Strong transcription	Thymus	Thymus
32	chr2:128013400-128020600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr2:128013400-128020600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:128013400-128020800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:128013400-128020800	Strong transcription	Left Ventricle	heart
36	chr2:128013400-128022400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:128013600-128018800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:128013600-128019000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:128013600-128019000	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:128013600-128019800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:128013600-128020800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:128013600-128020800	Strong transcription	Liver	Liver
43	chr2:128013600-128036200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:128013800-128019200	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr2:128013800-128019600	Strong transcription	NH-A	brain
46	chr2:128013800-128020200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:128014000-128018600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:128014000-128018800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:128014000-128019000	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr2:128014000-128019000	Strong transcription	Brain Anterior Caudate	brain

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