Variant report

Variant	rs10975116
Chromosome Location	chr9:5435079-5435080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5434272..5436176-chr9:5438552..5440389,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10739074	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10739075	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10758688	0.86[EUR][1000 genomes]
rs10758689	0.84[EUR][1000 genomes]
rs10815221	0.86[EUR][1000 genomes]
rs10815222	0.86[EUR][1000 genomes]
rs10815223	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10975112	0.86[EUR][1000 genomes]
rs10975113	0.81[EUR][1000 genomes]
rs10975114	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1322250	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2093455	0.83[EUR][1000 genomes]
rs2093456	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2295870	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3780392	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4742092	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7023253	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7862054	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892136	chr9:4921639-5436461	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv529689	chr9:4970093-5483250	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv892141	chr9:5116616-5479822	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1017126	chr9:5117847-5695486	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv539964	chr9:5117847-5695486	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv949627	chr9:5174829-5712626	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv427837	chr9:5189756-5454512	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv2759660	chr9:5288908-5454512	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv2758177	chr9:5297921-5454512	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv466108	chr9:5345673-5514372	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
11	nsv613196	chr9:5345673-5514372	Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
12	esv3330820	chr9:5366750-5510260	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5376000-5436800	Weak transcription	Psoas Muscle	Psoas
2	chr9:5408800-5435400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:5409800-5436400	Weak transcription	Small Intestine	intestine
4	chr9:5410000-5435400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr9:5410000-5435400	Weak transcription	Dnd41	blood
6	chr9:5415400-5437000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:5416800-5435400	Weak transcription	Fetal Lung	lung
8	chr9:5418400-5436600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr9:5419000-5435400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:5419000-5435400	Weak transcription	HSMMtube	muscle
11	chr9:5419200-5435400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:5419200-5437000	Weak transcription	Aorta	Aorta
13	chr9:5419200-5437000	Weak transcription	Pancreas	Pancrea
14	chr9:5419600-5435400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:5420000-5436800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr9:5423600-5435600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:5425000-5435600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:5425200-5435600	Weak transcription	Fetal Heart	heart
19	chr9:5425400-5435800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr9:5425600-5435400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:5426000-5435600	Weak transcription	A549	lung
22	chr9:5426200-5435400	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:5426200-5436400	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr9:5426400-5435400	Weak transcription	Fetal Kidney	kidney
25	chr9:5426600-5435400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr9:5427000-5435600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:5427600-5436000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr9:5428000-5435600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr9:5428000-5436600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr9:5428200-5436000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr9:5428600-5435400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:5428600-5435600	Weak transcription	HMEC	breast
33	chr9:5429400-5435800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr9:5429600-5436600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:5430000-5435400	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr9:5430200-5435400	Weak transcription	Adipose Nuclei	Adipose
37	chr9:5430200-5435400	Weak transcription	Osteobl	bone
38	chr9:5430400-5435400	Weak transcription	Brain Angular Gyrus	brain
39	chr9:5430400-5436600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr9:5430600-5436400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr9:5430800-5435400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr9:5430800-5436000	Weak transcription	Brain Substantia Nigra	brain
43	chr9:5430800-5436600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:5431000-5435400	Weak transcription	HSMM	muscle
45	chr9:5431200-5435400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr9:5431200-5435400	Weak transcription	HepG2	liver
47	chr9:5431200-5437000	Weak transcription	Brain Anterior Caudate	brain
48	chr9:5431800-5435400	Weak transcription	Primary B cells from peripheral blood	blood
49	chr9:5431800-5435400	Weak transcription	GM12878-XiMat	blood
50	chr9:5431800-5435800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links