Variant report

Variant	rs1475797
Chromosome Location	chr13:80093825-80093826
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:80088753..80091957-chr13:80093652..80097974,3	K562	blood:

Extended variants
information (count: 144 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1208049	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1212082	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12871015	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12877507	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1324868	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1335368	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1335370	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1408049	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1408658	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1410336	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1414155	0.91[ASN][1000 genomes]
rs1414156	0.91[ASN][1000 genomes]
rs1577416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1577418	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17071512	1.00[YRI][hapmap]
rs17071545	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs1748761	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs1752648	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs1752649	0.82[JPT][hapmap]
rs1853830	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2025913	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2057573	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2065743	0.92[ASN][1000 genomes]
rs2181433	0.81[ASN][1000 genomes]
rs2182009	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2182010	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2182873	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2265377	0.93[JPT][hapmap]
rs2265378	0.81[CHB][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap]
rs2274555	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2476172	0.83[ASN][1000 genomes]
rs2476173	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2484343	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2484344	0.83[ASN][1000 genomes]
rs2484345	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2760101	0.91[ASN][1000 genomes]
rs2760102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2760103	0.91[ASN][1000 genomes]
rs2760105	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2760106	0.88[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2763809	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs2763810	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2783119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2783120	0.94[ASN][1000 genomes]
rs2783121	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2783122	0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2783125	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2783126	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2876740	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs314688	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3187338	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3742117	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs3742118	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs3742119	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap]
rs3742122	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs3752994	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs386603	0.80[ASN][1000 genomes]
rs3903388	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs4145207	0.91[ASN][1000 genomes]
rs4146473	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs4476060	0.82[ASN][1000 genomes]
rs4885633	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4885634	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4885636	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs643778	0.81[CHB][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap]
rs6563100	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6563104	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs6563110	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6563113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6563115	0.94[ASN][1000 genomes]
rs6563116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs700396	0.90[ASN][1000 genomes]
rs7317416	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7319252	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs7319320	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7321953	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7322167	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7322673	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs73235963	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7325095	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7327386	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs7327603	0.82[JPT][hapmap]
rs7328494	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs7329331	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7331872	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7332367	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7332913	0.82[JPT][hapmap]
rs7336581	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7338530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7339303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7981067	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7982263	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7987193	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs7987769	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7988601	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7988784	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7990344	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7996493	0.89[ASN][1000 genomes]
rs7996652	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs7998837	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs8001281	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs8002042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs912639	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs9318621	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9318623	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9318625	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9318626	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap]
rs9318627	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap]
rs9318634	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9318640	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs9318641	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs9318644	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9530899	0.84[CHB][hapmap]
rs9530901	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9530913	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9530914	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9530922	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9530925	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9545067	0.81[CHB][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap]
rs9545076	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9545083	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9545085	0.82[JPT][hapmap]
rs9545086	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs9545087	0.92[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9545097	0.92[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap]
rs9545101	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs9545142	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9565489	0.82[JPT][hapmap]
rs9565497	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs9565510	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9574409	0.81[CHB][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap]
rs9574413	1.00[YRI][hapmap]
rs9574416	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs9574422	0.92[CEU][hapmap];0.80[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap]
rs9574429	0.82[ASN][1000 genomes]
rs9574434	0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9593396	0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap]
rs9593399	0.82[ASN][1000 genomes]
rs9601240	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9601242	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs987284	0.82[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv916983	chr13:80065879-80249702	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1475797	RP11-25J23.3	cis	Thyroid	GTEx
rs1475797	DERA	trans	parietal	SCAN
rs1475797	RP11-25J23.3	cis	lung	GTEx
rs1475797	SLAIN1	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80066800-80122800	Weak transcription	Esophagus	oesophagus
2	chr13:80067200-80095000	Weak transcription	HSMM	muscle
3	chr13:80070600-80096600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:80076000-80099200	Weak transcription	Hela-S3	cervix
5	chr13:80077600-80095600	Weak transcription	Fetal Intestine Large	intestine
6	chr13:80078000-80097200	Weak transcription	Psoas Muscle	Psoas
7	chr13:80078000-80097800	Weak transcription	Ovary	ovary
8	chr13:80078200-80102000	Weak transcription	Right Ventricle	heart
9	chr13:80079600-80098200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr13:80082800-80096600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr13:80082800-80096600	Weak transcription	Lung	lung
12	chr13:80082800-80108000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:80083000-80095200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr13:80083000-80120000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:80083000-80122800	Weak transcription	Stomach Mucosa	stomach
16	chr13:80083200-80095000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr13:80083200-80095000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:80083400-80096200	Weak transcription	Left Ventricle	heart
19	chr13:80085000-80096800	Weak transcription	Primary T cells from cord blood	blood
20	chr13:80086800-80098400	Weak transcription	Brain Substantia Nigra	brain
21	chr13:80087000-80095000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr13:80087400-80095200	Weak transcription	Liver	Liver
23	chr13:80087400-80134000	Weak transcription	Aorta	Aorta
24	chr13:80087400-80134600	Weak transcription	Pancreas	Pancrea
25	chr13:80087800-80095000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr13:80087800-80096600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr13:80088000-80095200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:80089000-80096600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:80089200-80098800	Weak transcription	Brain Angular Gyrus	brain
30	chr13:80089400-80097800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:80089400-80098800	Weak transcription	Brain Anterior Caudate	brain
32	chr13:80089400-80098800	Weak transcription	Brain Hippocampus Middle	brain
33	chr13:80089400-80099200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr13:80089400-80118400	Weak transcription	Small Intestine	intestine
35	chr13:80089800-80094800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr13:80090000-80095000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:80090400-80096600	Weak transcription	HUVEC	blood vessel
38	chr13:80090600-80112000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr13:80090800-80103400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr13:80091000-80099200	Weak transcription	K562	blood
41	chr13:80091400-80096600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr13:80091400-80108000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr13:80091600-80097800	Weak transcription	Fetal Heart	heart
44	chr13:80091600-80097800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr13:80092200-80094000	Enhancers	Osteobl	bone
46	chr13:80092200-80109400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr13:80092400-80096200	Weak transcription	Fetal Kidney	kidney
48	chr13:80092400-80096200	Weak transcription	GM12878-XiMat	blood
49	chr13:80092400-80099200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr13:80092400-80102000	Weak transcription	Colonic Mucosa	Colon

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