Variant report

Variant	rs9576154
Chromosome Location	chr13:37581051-37581052
allele	G/T
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	POLR2A	chr13:37580916-37581068	K562	blood:	n/a	n/a
2	POLR2A	chr13:37580888-37581058	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr13:37572075-37586589	K562	blood:	n/a	n/a
4	POLR2A	chr13:37580934-37581407	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr13:37580677-37581738	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr13:37581014-37581377	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:37570200..37576399-chr13:37580273..37587423,15	MCF-7	breast:

Variant related genes	Relation type
EXOSC8	TF binding region
ENSG00000120697	Chromatin interaction
ENSG00000120699	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1199951	1.00[AFR][1000 genomes]
rs1199962	0.90[CEU][hapmap]
rs1199963	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs1199972	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1199974	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1199975	1.00[YRI][hapmap]
rs1199981	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs1199982	0.90[CEU][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1199983	0.90[CEU][hapmap];0.91[AFR][1000 genomes]
rs1199984	0.90[CEU][hapmap]
rs1199987	0.84[AFR][1000 genomes]
rs12865199	0.90[EUR][1000 genomes]
rs1543738	0.90[CEU][hapmap]
rs1764483	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs1924419	0.99[EUR][1000 genomes]
rs1924420	0.97[EUR][1000 genomes]
rs1924421	0.83[EUR][1000 genomes]
rs1924422	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1924426	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1937761	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2093817	0.90[CEU][hapmap]
rs2147169	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2181787	0.95[EUR][1000 genomes]
rs2181788	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2186157	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2323165	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2769543	0.80[CEU][hapmap]
rs2785620	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs2801799	0.91[AFR][1000 genomes]
rs4291799	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4624036	0.81[EUR][1000 genomes]
rs483304	0.81[EUR][1000 genomes]
rs4941854	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4941855	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4941856	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4943441	0.90[CEU][hapmap]
rs568992	0.85[EUR][1000 genomes]
rs587505	0.81[CEU][hapmap]
rs6420362	1.00[YRI][hapmap]
rs6563506	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs6563507	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6563508	0.90[CEU][hapmap];0.81[AMR][1000 genomes]
rs675108	0.82[CEU][hapmap]
rs688280	0.81[CEU][hapmap]
rs71432622	0.86[EUR][1000 genomes]
rs73175079	1.00[AFR][1000 genomes]
rs7317750	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7321129	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7329314	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7334233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7338929	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7339296	0.81[AMR][1000 genomes]
rs7982674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7983986	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7984730	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7989205	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7989380	0.90[CEU][hapmap]
rs7991057	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7991181	0.99[EUR][1000 genomes]
rs7997310	0.90[CEU][hapmap]
rs9315458	0.88[EUR][1000 genomes]
rs9315459	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9531998	0.99[EUR][1000 genomes]
rs9532001	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9532002	0.99[EUR][1000 genomes]
rs9532004	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9532005	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9547707	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9547712	0.99[EUR][1000 genomes]
rs9547715	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9547717	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9547718	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9576153	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9594181	0.99[EUR][1000 genomes]
rs9603121	1.00[CEU][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv522336	chr13:37305641-37584838	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9576154	FAM48A	Cis_1M	lymphoblastoid	RTeQTL
rs9576154	SUPT20H	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37575400-37583800	Weak transcription	Spleen	Spleen
2	chr13:37575400-37631200	Weak transcription	Stomach Mucosa	stomach
3	chr13:37575600-37583800	Weak transcription	Esophagus	oesophagus
4	chr13:37575600-37583800	Weak transcription	Gastric	stomach
5	chr13:37575600-37592800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:37576000-37582400	Weak transcription	Colonic Mucosa	Colon
7	chr13:37576000-37583800	Weak transcription	Pancreas	Pancrea
8	chr13:37576000-37592600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:37576200-37581400	Weak transcription	Fetal Brain Male	brain
10	chr13:37576200-37606200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr13:37576200-37623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr13:37576400-37581600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:37576400-37582200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr13:37576400-37582400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr13:37576400-37583800	Weak transcription	Fetal Heart	heart
16	chr13:37576400-37588600	Weak transcription	Hela-S3	cervix
17	chr13:37576400-37595400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr13:37576400-37607600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr13:37576400-37608600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:37576400-37618800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:37576400-37623800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr13:37576600-37582400	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:37576600-37586800	Strong transcription	HSMM	muscle
24	chr13:37576600-37587400	Strong transcription	Placenta	Placenta
25	chr13:37576600-37600400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr13:37576600-37608400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:37576600-37623000	Strong transcription	Liver	Liver
28	chr13:37576600-37625800	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr13:37576800-37581800	Genic enhancers	Dnd41	blood
30	chr13:37576800-37584400	Strong transcription	NHEK	skin
31	chr13:37576800-37586200	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr13:37576800-37588400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr13:37576800-37600600	Strong transcription	HUVEC	blood vessel
34	chr13:37576800-37603000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr13:37576800-37609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr13:37576800-37621200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr13:37576800-37623200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr13:37577000-37582000	Strong transcription	A549	lung
39	chr13:37577000-37584200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr13:37577000-37585000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr13:37577000-37585400	Strong transcription	Fetal Lung	lung
42	chr13:37577000-37585400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr13:37577000-37586400	Strong transcription	Primary B cells from cord blood	blood
44	chr13:37577000-37586400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr13:37577000-37586400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:37577000-37586400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr13:37577000-37587600	Strong transcription	HepG2	liver
48	chr13:37577000-37588200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr13:37577000-37588400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr13:37577000-37591600	Strong transcription	NH-A	brain

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