Variant report

Variant	rs1199972
Chromosome Location	chr13:37627517-37627518
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1199951	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199956	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199960	0.87[EUR][1000 genomes]
rs1199962	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1199963	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199966	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1199974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199977	0.87[EUR][1000 genomes]
rs1199978	0.87[EUR][1000 genomes]
rs1199979	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1199980	0.87[EUR][1000 genomes]
rs1199981	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199982	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199983	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199984	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199986	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199987	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199988	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199989	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12429860	0.80[EUR][1000 genomes]
rs1336755	0.95[EUR][1000 genomes]
rs1543738	0.95[EUR][1000 genomes]
rs1764481	0.87[EUR][1000 genomes]
rs1764483	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1764484	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1764486	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1764487	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1764488	0.88[EUR][1000 genomes]
rs1924418	0.97[EUR][1000 genomes]
rs1924426	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1937760	0.88[EUR][1000 genomes]
rs2093817	0.97[EUR][1000 genomes]
rs2147169	0.87[AMR][1000 genomes]
rs2211618	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2323165	0.81[AMR][1000 genomes]
rs2323392	0.91[EUR][1000 genomes]
rs2669893	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2785620	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2801799	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2997189	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2997190	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2997193	0.83[EUR][1000 genomes]
rs3858859	0.96[EUR][1000 genomes]
rs4291799	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4941854	0.87[AMR][1000 genomes]
rs4941855	0.87[AMR][1000 genomes]
rs6563507	0.87[AMR][1000 genomes]
rs6563508	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6563509	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73175079	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7320899	0.97[EUR][1000 genomes]
rs7326688	0.95[EUR][1000 genomes]
rs7334233	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7339296	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7982674	0.81[AMR][1000 genomes]
rs7989380	0.95[EUR][1000 genomes]
rs7991057	0.81[AMR][1000 genomes]
rs7995098	0.87[EUR][1000 genomes]
rs7997310	0.97[EUR][1000 genomes]
rs8001662	0.97[EUR][1000 genomes]
rs9315459	0.81[AMR][1000 genomes]
rs9532005	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9547721	0.98[EUR][1000 genomes]
rs9547725	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9576153	0.81[AMR][1000 genomes]
rs9576154	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9576162	0.95[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1199972	SUPT20H	cis	Whole Blood	GTEx
rs1199972	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37575400-37631200	Weak transcription	Stomach Mucosa	stomach
2	chr13:37606800-37632400	Weak transcription	Hela-S3	cervix
3	chr13:37607800-37631000	Weak transcription	Pancreas	Pancrea
4	chr13:37608800-37631800	Weak transcription	Psoas Muscle	Psoas
5	chr13:37610000-37631000	Weak transcription	Lung	lung
6	chr13:37610000-37632200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr13:37610600-37632000	Weak transcription	Small Intestine	intestine
8	chr13:37611400-37631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr13:37613600-37632400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr13:37613600-37632600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr13:37616400-37632200	Weak transcription	A549	lung
12	chr13:37616800-37631000	Weak transcription	Right Ventricle	heart
13	chr13:37616800-37632200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr13:37616800-37632200	Weak transcription	NHLF	lung
15	chr13:37617000-37632400	Weak transcription	K562	blood
16	chr13:37617400-37631000	Weak transcription	NHEK	skin
17	chr13:37617600-37632600	Weak transcription	Brain Substantia Nigra	brain
18	chr13:37617600-37632800	Weak transcription	Brain Hippocampus Middle	brain
19	chr13:37617600-37632800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr13:37617600-37632800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr13:37617800-37631800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr13:37618000-37631800	Weak transcription	Gastric	stomach
23	chr13:37618000-37632200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr13:37618000-37632400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr13:37618000-37632400	Weak transcription	Brain Angular Gyrus	brain
26	chr13:37618000-37632400	Weak transcription	Fetal Kidney	kidney
27	chr13:37618000-37632600	Weak transcription	Thymus	Thymus
28	chr13:37618000-37632800	Weak transcription	Ovary	ovary
29	chr13:37618000-37633000	Weak transcription	Spleen	Spleen
30	chr13:37618200-37630600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr13:37618200-37630800	Weak transcription	Fetal Stomach	stomach
32	chr13:37618200-37630800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr13:37618200-37631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr13:37618200-37631000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:37618200-37632200	Weak transcription	Brain Germinal Matrix	brain
36	chr13:37618200-37632400	Weak transcription	Fetal Brain Male	brain
37	chr13:37618200-37632600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr13:37618200-37633000	Weak transcription	Esophagus	oesophagus
39	chr13:37618800-37632200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:37619400-37632000	Weak transcription	Fetal Heart	heart
41	chr13:37619600-37631800	Weak transcription	HepG2	liver
42	chr13:37620800-37631800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr13:37620800-37632200	Weak transcription	Brain Anterior Caudate	brain
44	chr13:37621200-37631000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr13:37621600-37630600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr13:37621600-37631000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr13:37621600-37631000	Weak transcription	Fetal Brain Female	brain
48	chr13:37621600-37631000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr13:37621600-37631000	Weak transcription	Fetal Muscle Leg	muscle
50	chr13:37621600-37631000	Weak transcription	Left Ventricle	heart

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