Variant report

Variant	rs6563509
Chromosome Location	chr13:37611969-37611970
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	chr13:37573406..37575102-chr13:37611578..37613233,2	MCF-7	breast:
2	chr13:37611847..37614707-chr13:37631695..37633641,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120699	Chromatin interaction
ENSG00000102710	Chromatin interaction
ENSG00000120697	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1199951	0.94[EUR][1000 genomes]
rs1199956	0.95[EUR][1000 genomes]
rs1199960	0.84[EUR][1000 genomes]
rs1199962	0.88[EUR][1000 genomes]
rs1199963	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1199966	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1199972	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199974	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1199977	0.87[EUR][1000 genomes]
rs1199978	0.87[EUR][1000 genomes]
rs1199979	0.91[EUR][1000 genomes]
rs1199980	0.87[EUR][1000 genomes]
rs1199981	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199982	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1199983	0.90[EUR][1000 genomes]
rs1199984	0.94[EUR][1000 genomes]
rs1199986	0.94[EUR][1000 genomes]
rs1199987	0.94[EUR][1000 genomes]
rs1199988	0.95[EUR][1000 genomes]
rs1199989	0.95[EUR][1000 genomes]
rs1211337	0.84[AFR][1000 genomes]
rs12429860	0.80[EUR][1000 genomes]
rs1336755	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1543738	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17054796	0.81[AFR][1000 genomes]
rs17054831	0.84[AFR][1000 genomes]
rs1764481	0.84[EUR][1000 genomes]
rs1764483	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1764484	0.94[EUR][1000 genomes]
rs1764486	0.94[EUR][1000 genomes]
rs1764487	0.95[EUR][1000 genomes]
rs1764488	0.85[EUR][1000 genomes]
rs1924418	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1924426	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1937760	0.85[EUR][1000 genomes]
rs1937761	0.81[AMR][1000 genomes]
rs2093817	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2211618	0.95[EUR][1000 genomes]
rs2323392	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2669893	0.95[EUR][1000 genomes]
rs2785620	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2997189	0.94[EUR][1000 genomes]
rs2997190	0.94[EUR][1000 genomes]
rs2997193	0.81[EUR][1000 genomes]
rs3858859	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4941856	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6563508	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73175079	0.93[EUR][1000 genomes]
rs7317750	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7320899	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7326688	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7329314	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7338929	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7339296	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7983986	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7984730	0.81[AMR][1000 genomes]
rs7989205	0.81[AMR][1000 genomes]
rs7989380	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7991181	0.83[AFR][1000 genomes]
rs7995098	0.84[EUR][1000 genomes]
rs7995985	0.87[AFR][1000 genomes]
rs7997310	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8001662	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9285111	0.84[AFR][1000 genomes]
rs9547715	0.82[AFR][1000 genomes]
rs9547718	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9547721	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9547725	0.94[EUR][1000 genomes]
rs9576162	0.86[AMR][1000 genomes];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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6563509	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr13:37576200-37623800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr13:37576400-37618800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr13:37576400-37623800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr13:37576600-37623000	Strong transcription	Liver	Liver
6	chr13:37576600-37625800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr13:37576800-37621200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr13:37576800-37623200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr13:37577000-37623000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:37577000-37623400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr13:37577000-37624400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr13:37577200-37623200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr13:37577200-37625200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr13:37577200-37625800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr13:37577200-37625800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr13:37577600-37623600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr13:37578200-37615200	Weak transcription	K562	blood
18	chr13:37581800-37622800	Strong transcription	Dnd41	blood
19	chr13:37583000-37622800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr13:37583000-37623400	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr13:37583200-37622600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr13:37585400-37616000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr13:37586800-37623400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr13:37587000-37622200	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr13:37587800-37618000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr13:37587800-37622600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr13:37588400-37622400	Strong transcription	Adipose Nuclei	Adipose
28	chr13:37588600-37619600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:37588800-37614200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:37589200-37625800	Strong transcription	Fetal Thymus	thymus
31	chr13:37589400-37622600	Strong transcription	Placenta	Placenta
32	chr13:37589600-37623800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr13:37592200-37622600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr13:37592400-37618000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr13:37592400-37619400	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr13:37594600-37622400	Strong transcription	Primary B cells from cord blood	blood
37	chr13:37596800-37615800	Weak transcription	Right Ventricle	heart
38	chr13:37598200-37613200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr13:37599600-37623000	Strong transcription	HSMM	muscle
40	chr13:37601000-37617600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr13:37601200-37618000	Strong transcription	Fetal Lung	lung
42	chr13:37601400-37614200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr13:37601800-37625200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr13:37602200-37612000	Strong transcription	Fetal Muscle Leg	muscle
45	chr13:37602200-37618000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr13:37602200-37621600	Strong transcription	Primary T cells from cord blood	blood
47	chr13:37602600-37621000	Strong transcription	Fetal Intestine Large	intestine
48	chr13:37602800-37612000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr13:37602800-37612000	Strong transcription	HepG2	liver
50	chr13:37602800-37622200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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