Variant report

Variant	rs9534961
Chromosome Location	chr13:48701727-48701728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:48699791..48701877-chr13:48806466..48810071,5	MCF-7	breast:
2	chr13:48701521..48703483-chr13:48708256..48709963,2	K562	blood:
3	chr13:48700736..48702519-chr13:48877364..48879674,2	MCF-7	breast:
4	chr13:48700823..48701797-chr13:48806881..48808213,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139687	Chromatin interaction
ENSG00000136156	Chromatin interaction
ENSG00000224510	Chromatin interaction
ENSG00000231473	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11616639	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1410117	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1571256	0.85[ASN][1000 genomes]
rs1927213	0.86[ASN][1000 genomes]
rs2094192	0.84[ASN][1000 genomes]
rs2104480	0.83[ASN][1000 genomes]
rs2148246	0.83[ASN][1000 genomes]
rs2148938	0.85[ASN][1000 genomes]
rs2406709	0.83[ASN][1000 genomes]
rs2406797	0.86[ASN][1000 genomes]
rs4294712	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4941623	0.84[ASN][1000 genomes]
rs4942748	0.86[ASN][1000 genomes]
rs55633570	0.84[AMR][1000 genomes]
rs56399021	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61973324	0.97[AMR][1000 genomes]
rs7324484	0.84[ASN][1000 genomes]
rs7326363	0.86[ASN][1000 genomes]
rs7336214	0.86[ASN][1000 genomes]
rs8001243	0.85[ASN][1000 genomes]
rs9526442	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526443	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526445	0.86[ASN][1000 genomes]
rs9526447	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526449	0.88[ASN][1000 genomes]
rs9526451	0.82[ASN][1000 genomes]
rs9534895	0.80[AMR][1000 genomes]
rs9534900	0.84[AMR][1000 genomes]
rs9534931	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9534933	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534937	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534939	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534943	0.84[ASN][1000 genomes]
rs9534944	0.84[ASN][1000 genomes]
rs9534945	0.84[ASN][1000 genomes]
rs9534946	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9534947	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9534948	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9534950	0.85[ASN][1000 genomes]
rs9534951	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9534952	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9534957	0.86[ASN][1000 genomes]
rs9534965	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9562802	0.84[ASN][1000 genomes]
rs9567987	0.83[ASN][1000 genomes]
rs9567991	0.83[ASN][1000 genomes]
rs9567994	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	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48697800-48702200	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr13:48699600-48702000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr13:48699600-48702200	Enhancers	Rectal Smooth Muscle	rectum
4	chr13:48699800-48701800	Enhancers	Fetal Kidney	kidney
5	chr13:48700000-48702000	Enhancers	Liver	Liver
6	chr13:48700400-48702200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr13:48700400-48702200	Enhancers	Colon Smooth Muscle	Colon
8	chr13:48700400-48705600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:48700600-48702000	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr13:48701000-48701800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:48701000-48701800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr13:48701000-48701800	Enhancers	Stomach Mucosa	stomach
13	chr13:48701000-48701800	Enhancers	HMEC	breast
14	chr13:48701000-48702000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr13:48701000-48702000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr13:48701000-48702000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr13:48701000-48702000	Enhancers	Brain Substantia Nigra	brain
18	chr13:48701000-48702000	Enhancers	Fetal Muscle Leg	muscle
19	chr13:48701000-48702000	Enhancers	Fetal Stomach	stomach
20	chr13:48701000-48702000	Enhancers	Fetal Thymus	thymus
21	chr13:48701000-48702200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr13:48701000-48702200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr13:48701000-48702200	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr13:48701000-48702200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr13:48701200-48701800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr13:48701200-48701800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr13:48701200-48701800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:48701200-48701800	Enhancers	Placenta	Placenta
29	chr13:48701200-48702000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr13:48701200-48702000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr13:48701200-48702000	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr13:48701200-48702000	Enhancers	Primary B cells from cord blood	blood
33	chr13:48701200-48702000	Enhancers	Primary B cells from peripheral blood	blood
34	chr13:48701200-48702000	Enhancers	Primary T cells from cord blood	blood
35	chr13:48701200-48702000	Enhancers	Primary T cells fromperipheralblood	blood
36	chr13:48701200-48702000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr13:48701200-48702000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr13:48701200-48702000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr13:48701200-48702000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr13:48701200-48702000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr13:48701200-48702000	Enhancers	Brain Cingulate Gyrus	brain
42	chr13:48701200-48702000	Enhancers	Duodenum Mucosa	Duodenum
43	chr13:48701200-48702000	Enhancers	Psoas Muscle	Psoas
44	chr13:48701200-48702000	Enhancers	Right Atrium	heart
45	chr13:48701200-48702000	Enhancers	Thymus	Thymus
46	chr13:48701200-48702000	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr13:48701200-48702000	Enhancers	NHEK	skin
48	chr13:48701200-48702200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr13:48701200-48702200	Enhancers	H1 Cell Line	embryonic stem cell
50	chr13:48701200-48702200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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