Variant report

Variant	rs6563506
Chromosome Location	chr13:37526560-37526561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10507444	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1199962	0.81[CEU][hapmap]
rs1199963	0.81[CEU][hapmap]
rs1199974	0.81[CEU][hapmap]
rs1199981	0.81[CEU][hapmap]
rs1199982	0.81[CEU][hapmap]
rs1199983	0.81[CEU][hapmap]
rs1199984	0.81[CEU][hapmap]
rs1199997	1.00[ASN][1000 genomes]
rs1199998	1.00[ASN][1000 genomes]
rs1200000	1.00[ASN][1000 genomes]
rs1200001	1.00[ASN][1000 genomes]
rs1200002	1.00[ASN][1000 genomes]
rs1200003	1.00[ASN][1000 genomes]
rs1336165	1.00[ASN][1000 genomes]
rs1543738	0.88[ASW][hapmap];0.81[CEU][hapmap];0.91[LWK][hapmap];0.81[YRI][hapmap]
rs17054770	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17054775	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17054789	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17054790	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17054829	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17054838	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17054925	1.00[ASN][1000 genomes]
rs17054972	1.00[ASN][1000 genomes]
rs1764483	0.81[CEU][hapmap]
rs1924418	0.81[LWK][hapmap];0.87[MKK][hapmap];0.87[YRI][hapmap]
rs1924419	0.84[EUR][1000 genomes]
rs1924420	0.83[EUR][1000 genomes]
rs1924421	0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924422	0.91[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs1937761	0.91[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs2093817	0.81[CEU][hapmap];0.82[LWK][hapmap];0.87[MKK][hapmap]
rs2147169	0.91[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2181787	0.81[EUR][1000 genomes]
rs2181788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2186157	0.82[EUR][1000 genomes]
rs2323165	0.91[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2769542	1.00[CHB][hapmap]
rs2785620	0.81[CEU][hapmap]
rs4291799	0.91[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs4624036	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941854	0.91[CEU][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4941855	0.81[EUR][1000 genomes]
rs4941856	0.91[CEU][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.82[EUR][1000 genomes]
rs4943441	0.81[CEU][hapmap];0.81[MKK][hapmap]
rs57719094	1.00[ASN][1000 genomes]
rs59899061	1.00[ASN][1000 genomes]
rs59901477	1.00[ASN][1000 genomes]
rs608385	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6563507	0.91[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs6563508	0.81[CEU][hapmap]
rs7317750	0.91[CEU][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs7321129	0.91[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs7329314	0.84[EUR][1000 genomes]
rs7334233	0.83[EUR][1000 genomes]
rs7338929	0.91[CEU][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs73533924	1.00[ASN][1000 genomes]
rs73543820	1.00[ASN][1000 genomes]
rs7982674	0.83[EUR][1000 genomes]
rs7983986	0.91[CEU][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs7984730	0.81[EUR][1000 genomes]
rs7989205	0.88[ASW][hapmap];0.91[CEU][hapmap];0.93[LWK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7989380	0.81[CEU][hapmap]
rs7991057	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7991181	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7997310	0.81[CEU][hapmap];0.84[LWK][hapmap];0.87[MKK][hapmap]
rs8001410	1.00[ASN][1000 genomes]
rs9315459	0.83[EUR][1000 genomes]
rs9531998	0.84[EUR][1000 genomes]
rs9532000	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9532001	0.91[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs9532002	0.84[EUR][1000 genomes]
rs9532004	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs9532005	0.91[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs9547703	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[TSI][hapmap]
rs9547704	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs9547705	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9547707	0.91[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs9547712	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9547715	0.91[CEU][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.84[EUR][1000 genomes]
rs9547717	0.82[CEU][hapmap]
rs9547718	0.91[CEU][hapmap];0.89[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs9576153	0.83[EUR][1000 genomes]
rs9576154	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs9594181	0.84[EUR][1000 genomes]
rs9594184	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9603121	0.91[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs9603124	1.00[CHB][hapmap];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6563506	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37515400-37533000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:37517200-37538400	Weak transcription	Fetal Brain Male	brain
3	chr13:37517600-37529000	Weak transcription	Thymus	Thymus
4	chr13:37519400-37527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:37519400-37528800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:37520400-37538000	Weak transcription	Colonic Mucosa	Colon
8	chr13:37520600-37560800	Weak transcription	Small Intestine	intestine
9	chr13:37520800-37529000	Weak transcription	Gastric	stomach
10	chr13:37520800-37529400	Weak transcription	HMEC	breast
11	chr13:37520800-37538000	Weak transcription	HepG2	liver
12	chr13:37521000-37536600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr13:37521200-37538200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr13:37521400-37526800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:37521400-37527800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:37521400-37528600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr13:37521400-37528800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr13:37521400-37529200	Weak transcription	Fetal Kidney	kidney
19	chr13:37521400-37529400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr13:37521400-37531000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:37521400-37531000	Strong transcription	Liver	Liver
22	chr13:37521400-37532200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:37521400-37537800	Weak transcription	NHLF	lung
24	chr13:37521400-37538000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:37521400-37538400	Weak transcription	Aorta	Aorta
26	chr13:37521400-37542800	Weak transcription	A549	lung
27	chr13:37521600-37526600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr13:37521600-37527400	Strong transcription	Adipose Nuclei	Adipose
29	chr13:37521600-37527800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:37521600-37532600	Strong transcription	Primary T cells from cord blood	blood
31	chr13:37521600-37534800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr13:37521600-37535200	Weak transcription	NHEK	skin
33	chr13:37521600-37537800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr13:37521600-37538000	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr13:37521600-37538000	Weak transcription	Brain Hippocampus Middle	brain
36	chr13:37521600-37538200	Weak transcription	HSMMtube	muscle
37	chr13:37521800-37539200	Weak transcription	K562	blood
38	chr13:37522000-37531200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr13:37522000-37538000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr13:37522000-37538400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr13:37522200-37526600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr13:37522200-37527200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr13:37522200-37527600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr13:37522400-37531000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr13:37522600-37526800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr13:37522600-37527400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr13:37522600-37527600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr13:37522600-37541000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr13:37522600-37548800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr13:37522800-37526600	Strong transcription	HUES64 Cell Line	embryonic stem cell

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