Variant report

Variant	rs1199974
Chromosome Location	chr13:37625459-37625460
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr13:37625439-37625637	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:37573365..37576545-chr13:37622810..37625636,4	MCF-7	breast:
2	chr13:37623154..37627284-chr13:37630471..37633979,5	MCF-7	breast:

Variant related genes	Relation type
SUPT20H	TF binding region
ENSG00000120697	Chromatin interaction
ENSG00000120699	Chromatin interaction
ENSG00000102710	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1199951	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199956	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199960	0.84[EUR][1000 genomes]
rs1199962	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1199963	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199966	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1199972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199975	1.00[YRI][hapmap]
rs1199977	0.84[EUR][1000 genomes]
rs1199978	0.84[EUR][1000 genomes]
rs1199979	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1199980	0.84[EUR][1000 genomes]
rs1199981	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199982	1.00[CEU][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199983	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1199984	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1199986	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199987	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1199988	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1199989	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12429860	0.80[EUR][1000 genomes]
rs1336755	0.92[EUR][1000 genomes]
rs1543738	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs1764481	0.84[EUR][1000 genomes]
rs1764483	1.00[CEU][hapmap];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];0.94[EUR][1000 genomes]
rs1764487	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1764488	0.85[EUR][1000 genomes]
rs1924418	0.97[EUR][1000 genomes]
rs1924422	0.90[CEU][hapmap]
rs1924426	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1937760	0.85[EUR][1000 genomes]
rs1937761	0.90[CEU][hapmap]
rs2093817	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2147169	0.90[CEU][hapmap];0.87[AMR][1000 genomes]
rs2181788	0.81[CEU][hapmap]
rs2211618	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2323165	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs2323392	0.89[EUR][1000 genomes]
rs2669893	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2769543	0.89[CEU][hapmap]
rs2785620	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2801799	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2997189	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2997190	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2997193	0.81[EUR][1000 genomes]
rs3858859	0.93[EUR][1000 genomes]
rs4291799	0.90[CEU][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4941854	0.90[CEU][hapmap];0.87[AMR][1000 genomes]
rs4941855	0.87[AMR][1000 genomes]
rs4941856	0.90[CEU][hapmap]
rs4943441	1.00[CEU][hapmap]
rs6420362	1.00[YRI][hapmap]
rs6563506	0.81[CEU][hapmap]
rs6563507	0.90[CEU][hapmap];0.87[AMR][1000 genomes]
rs6563508	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6563509	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs675108	0.82[CEU][hapmap]
rs73175079	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7317750	0.90[CEU][hapmap]
rs7320899	0.97[EUR][1000 genomes]
rs7321129	0.90[CEU][hapmap]
rs7326688	0.92[EUR][1000 genomes]
rs7334233	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7338929	0.90[CEU][hapmap]
rs7339296	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7982674	0.81[AMR][1000 genomes]
rs7983986	0.90[CEU][hapmap]
rs7989205	0.90[CEU][hapmap]
rs7989380	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7991057	0.90[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs7995098	0.84[EUR][1000 genomes]
rs7997310	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs8001662	0.97[EUR][1000 genomes]
rs9315459	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs9532001	0.90[CEU][hapmap]
rs9532004	0.90[CEU][hapmap]
rs9532005	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9547707	0.90[CEU][hapmap]
rs9547715	0.90[CEU][hapmap]
rs9547717	0.81[CEU][hapmap]
rs9547718	0.90[CEU][hapmap]
rs9547721	0.95[EUR][1000 genomes]
rs9547725	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9576153	0.81[AMR][1000 genomes]
rs9576154	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9576162	0.92[EUR][1000 genomes]
rs9603121	0.90[CEU][hapmap]

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
rs1199974	SUPT20H	cis	Whole Blood	GTEx
rs1199974	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 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	chr13:37576600-37625800	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr13:37577200-37625800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr13:37577200-37625800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr13:37589200-37625800	Strong transcription	Fetal Thymus	thymus
6	chr13:37606800-37632400	Weak transcription	Hela-S3	cervix
7	chr13:37607800-37631000	Weak transcription	Pancreas	Pancrea
8	chr13:37608800-37631800	Weak transcription	Psoas Muscle	Psoas
9	chr13:37610000-37631000	Weak transcription	Lung	lung
10	chr13:37610000-37632200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr13:37610200-37626000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:37610600-37632000	Weak transcription	Small Intestine	intestine
13	chr13:37610800-37625800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:37611400-37631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:37613600-37632400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr13:37613600-37632600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr13:37616400-37632200	Weak transcription	A549	lung
18	chr13:37616800-37631000	Weak transcription	Right Ventricle	heart
19	chr13:37616800-37632200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr13:37616800-37632200	Weak transcription	NHLF	lung
21	chr13:37617000-37627000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr13:37617000-37632400	Weak transcription	K562	blood
23	chr13:37617400-37631000	Weak transcription	NHEK	skin
24	chr13:37617600-37632600	Weak transcription	Brain Substantia Nigra	brain
25	chr13:37617600-37632800	Weak transcription	Brain Hippocampus Middle	brain
26	chr13:37617600-37632800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr13:37617600-37632800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr13:37617800-37631800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr13:37618000-37627400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr13:37618000-37631800	Weak transcription	Gastric	stomach
31	chr13:37618000-37632200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr13:37618000-37632400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr13:37618000-37632400	Weak transcription	Brain Angular Gyrus	brain
34	chr13:37618000-37632400	Weak transcription	Fetal Kidney	kidney
35	chr13:37618000-37632600	Weak transcription	Thymus	Thymus
36	chr13:37618000-37632800	Weak transcription	Ovary	ovary
37	chr13:37618000-37633000	Weak transcription	Spleen	Spleen
38	chr13:37618200-37630600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr13:37618200-37630800	Weak transcription	Fetal Stomach	stomach
40	chr13:37618200-37630800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr13:37618200-37631000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr13:37618200-37631000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:37618200-37632200	Weak transcription	Brain Germinal Matrix	brain
44	chr13:37618200-37632400	Weak transcription	Fetal Brain Male	brain
45	chr13:37618200-37632600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr13:37618200-37633000	Weak transcription	Esophagus	oesophagus
47	chr13:37618800-37632200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr13:37619400-37632000	Weak transcription	Fetal Heart	heart
49	chr13:37619600-37631800	Weak transcription	HepG2	liver
50	chr13:37620800-37631800	Weak transcription	Rectal Mucosa Donor 29	rectum

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