Variant report

Variant	rs6561415
Chromosome Location	chr13:48509954-48509955
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	POLR2A	chr13:48509926-48510119	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48508669..48510249-chr13:48511199..48513558,2	K562	blood:

Variant related genes	Relation type
LINC00562	TF binding region
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1041070	0.86[ASN][1000 genomes]
rs1544078	0.83[ASN][1000 genomes]
rs2094194	0.85[ASN][1000 genomes]
rs7336972	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7981260	0.82[AFR][1000 genomes]
rs7989231	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7994359	0.82[ASN][1000 genomes]
rs9534876	0.83[ASN][1000 genomes]
rs9567954	0.86[ASN][1000 genomes]
rs9567955	0.86[ASN][1000 genomes]
rs9595815	0.85[ASN][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	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6561415	SUCLA2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48492200-48510800	Weak transcription	Left Ventricle	heart
2	chr13:48501000-48531200	Weak transcription	Spleen	Spleen
3	chr13:48502000-48530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:48502600-48513600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr13:48503600-48512400	Weak transcription	Aorta	Aorta
6	chr13:48503800-48513200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:48503800-48516800	Weak transcription	NHDF-Ad	bronchial
8	chr13:48504000-48513400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:48506000-48531400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr13:48506800-48522600	Weak transcription	Fetal Brain Male	brain
11	chr13:48507200-48510800	Weak transcription	Primary T cells from cord blood	blood
12	chr13:48507200-48524000	Weak transcription	Lung	lung
13	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
14	chr13:48507400-48512200	Weak transcription	Adipose Nuclei	Adipose
15	chr13:48507600-48511400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:48507600-48511600	Weak transcription	A549	lung
17	chr13:48507600-48513400	Weak transcription	Fetal Lung	lung
18	chr13:48507800-48511800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr13:48507800-48513600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr13:48507800-48513600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr13:48507800-48515200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr13:48507800-48515200	Weak transcription	Osteobl	bone
23	chr13:48507800-48530600	Weak transcription	Brain Angular Gyrus	brain
24	chr13:48508000-48511400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr13:48508000-48514000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr13:48508000-48514200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr13:48508000-48514200	Weak transcription	Fetal Stomach	stomach
28	chr13:48508000-48515200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr13:48508000-48515200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr13:48508000-48515400	Weak transcription	Fetal Kidney	kidney
31	chr13:48508000-48516200	Weak transcription	Brain Substantia Nigra	brain
32	chr13:48508000-48522400	Weak transcription	GM12878-XiMat	blood
33	chr13:48508000-48531400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr13:48508200-48511000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr13:48508200-48511200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr13:48508200-48512400	Weak transcription	Fetal Muscle Leg	muscle
37	chr13:48508200-48512400	Weak transcription	Thymus	Thymus
38	chr13:48508200-48515400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr13:48508200-48515800	Weak transcription	Psoas Muscle	Psoas
40	chr13:48508200-48520000	Weak transcription	HepG2	liver
41	chr13:48508200-48529600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:48508400-48511400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr13:48508400-48511400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:48508400-48511400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr13:48508400-48512400	Weak transcription	Pancreas	Pancrea
46	chr13:48508400-48513200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr13:48508400-48513600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:48508400-48513600	Weak transcription	HMEC	breast
49	chr13:48508400-48515200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr13:48508600-48512200	Weak transcription	Monocytes-CD14+_RO01746	blood

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