Variant report

Variant	rs1199966
Chromosome Location	chr13:37630927-37630928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:37623154..37627284-chr13:37630471..37633979,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102710	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1199951	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1199956	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1199962	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1199963	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1199972	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1199974	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1199979	0.82[EUR][1000 genomes]
rs1199981	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1199982	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1199983	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1199984	0.85[EUR][1000 genomes]
rs1199986	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1199987	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1199988	0.86[EUR][1000 genomes]
rs1199989	0.86[EUR][1000 genomes]
rs1336755	0.86[EUR][1000 genomes]
rs1543738	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1764483	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1764484	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1764486	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1764487	0.86[EUR][1000 genomes]
rs1924418	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1924426	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2093817	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2211618	0.86[EUR][1000 genomes]
rs2323392	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2669893	0.86[EUR][1000 genomes]
rs2785620	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2997189	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2997190	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3858859	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6563508	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6563509	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73175079	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7320899	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7326688	0.86[EUR][1000 genomes]
rs7339296	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7989380	0.86[EUR][1000 genomes]
rs7997310	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8001662	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9547721	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9547725	0.85[EUR][1000 genomes]
rs9576162	0.86[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
rs1199966	SUPT20H	cis	Whole Blood	GTEx
rs1199966	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	chr13:37618200-37631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr13:37618200-37631000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:37618200-37632200	Weak transcription	Brain Germinal Matrix	brain
33	chr13:37618200-37632400	Weak transcription	Fetal Brain Male	brain
34	chr13:37618200-37632600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr13:37618200-37633000	Weak transcription	Esophagus	oesophagus
36	chr13:37618800-37632200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr13:37619400-37632000	Weak transcription	Fetal Heart	heart
38	chr13:37619600-37631800	Weak transcription	HepG2	liver
39	chr13:37620800-37631800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr13:37620800-37632200	Weak transcription	Brain Anterior Caudate	brain
41	chr13:37621200-37631000	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr13:37621600-37631000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr13:37621600-37631000	Weak transcription	Fetal Brain Female	brain
44	chr13:37621600-37631000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr13:37621600-37631000	Weak transcription	Fetal Muscle Leg	muscle
46	chr13:37621600-37631000	Weak transcription	Left Ventricle	heart
47	chr13:37621600-37631200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr13:37621600-37632200	Weak transcription	Primary T cells from cord blood	blood
49	chr13:37621600-37632400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr13:37622000-37631000	Weak transcription	Fetal Intestine Small	intestine

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