Variant report

Variant	rs11239310
Chromosome Location	chr10:45499974-45499975
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	chr10:45499672-45503840	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45495742..45497934-chr10:45498787..45500751,2	MCF-7	breast:
2	chr10:45499571..45502259-chr10:45742998..45745677,2	K562	blood:

Variant related genes	Relation type
C10orf25	TF binding region
ENSG00000165512	Chromatin interaction
ENSG00000165511	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10047345	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11239337	0.94[ASW][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11494	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12257275	0.89[EUR][1000 genomes]
rs12264627	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157327	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17157328	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2095088	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2104898	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4339993	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4573635	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56259997	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57046651	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59085162	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60581169	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61183370	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6593454	0.96[EUR][1000 genomes]
rs7080655	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7095202	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72782417	0.92[EUR][1000 genomes]
rs73283471	0.92[EUR][1000 genomes]
rs7902918	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7915377	0.98[EUR][1000 genomes]
rs7918953	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];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	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831848	chr10:45490176-45667670	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45497000-45511000	Weak transcription	Gastric	stomach
2	chr10:45497200-45500200	Weak transcription	Lung	lung
3	chr10:45497200-45504000	Weak transcription	Esophagus	oesophagus
4	chr10:45497400-45501200	Weak transcription	Aorta	Aorta
5	chr10:45497400-45501400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:45497400-45503800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr10:45497400-45504000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr10:45497400-45504000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr10:45497600-45500200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr10:45497600-45502800	Weak transcription	Fetal Brain Male	brain
11	chr10:45497600-45503800	Weak transcription	Brain Substantia Nigra	brain
12	chr10:45497600-45504000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr10:45497800-45500600	ZNF genes & repeats	Primary B cells from cord blood	blood
14	chr10:45497800-45500600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
15	chr10:45497800-45502200	Weak transcription	Right Ventricle	heart
16	chr10:45497800-45504000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr10:45498000-45500000	ZNF genes & repeats	Primary T cells from cord blood	blood
18	chr10:45498000-45500000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
19	chr10:45498000-45500200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:45498200-45500600	ZNF genes & repeats	GM12878-XiMat	blood
21	chr10:45498200-45503800	Weak transcription	Colon Smooth Muscle	Colon
22	chr10:45498200-45503800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr10:45498200-45504000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr10:45498400-45500200	Weak transcription	Osteobl	bone
25	chr10:45498400-45500400	Genic enhancers	Primary hematopoietic stem cells	blood
26	chr10:45498400-45500600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
27	chr10:45498400-45501200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr10:45498400-45503800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr10:45498600-45500400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr10:45498600-45500400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:45498600-45500800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
32	chr10:45498600-45501400	Strong transcription	Fetal Lung	lung
33	chr10:45498800-45500000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr10:45498800-45500000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:45498800-45500000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
36	chr10:45498800-45500000	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr10:45498800-45500000	ZNF genes & repeats	HMEC	breast
38	chr10:45498800-45500400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr10:45498800-45500400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
40	chr10:45498800-45500400	Strong transcription	Rectal Smooth Muscle	rectum
41	chr10:45498800-45500600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr10:45498800-45500600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr10:45498800-45500600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr10:45498800-45500600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
45	chr10:45498800-45500600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr10:45498800-45500600	Strong transcription	Brain Hippocampus Middle	brain
47	chr10:45498800-45500800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:45498800-45500800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr10:45498800-45501200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr10:45498800-45501200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links