Variant report

Variant	rs10039091
Chromosome Location	chr5:41852378-41852379
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:41850949..41853870-chr5:41854462..41856684,2	MCF-7	breast:
2	chr5:41843869..41846135-chr5:41851882..41853656,2	K562	blood:
3	chr5:41851290..41853624-chr5:41855397..41858252,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10038717	0.95[AFR][1000 genomes]
rs10042050	0.91[AFR][1000 genomes]
rs10045224	0.96[AFR][1000 genomes]
rs10051536	0.83[AFR][1000 genomes]
rs10061961	0.83[AFR][1000 genomes]
rs10064781	0.82[AFR][1000 genomes]
rs10071732	0.80[AFR][1000 genomes]
rs10072903	1.00[AFR][1000 genomes]
rs10079775	0.95[AFR][1000 genomes]
rs10080034	0.95[AFR][1000 genomes]
rs10214013	0.95[AFR][1000 genomes]
rs10473254	0.95[AFR][1000 genomes]
rs13354429	1.00[AFR][1000 genomes]
rs13357640	0.95[AFR][1000 genomes]
rs13358155	1.00[AFR][1000 genomes]
rs16872021	0.83[AFR][1000 genomes]
rs28429157	0.92[AFR][1000 genomes]
rs28588578	0.95[AFR][1000 genomes]
rs28661292	0.91[AFR][1000 genomes]
rs9292830	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830271	chr5:41716527-41895710	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv2762518	chr5:41780210-41935113	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
3	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
4	nsv4811	chr5:41844522-41887353	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 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	chr5:41819200-41852800	Weak transcription	Pancreas	Pancrea
2	chr5:41824600-41859400	Weak transcription	Spleen	Spleen
3	chr5:41831200-41854400	Weak transcription	Colonic Mucosa	Colon
4	chr5:41832800-41869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:41836000-41857200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:41836600-41863800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr5:41837200-41858600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:41841800-41869200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:41843800-41855600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:41849000-41853000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:41849000-41853800	Strong transcription	NHDF-Ad	bronchial
12	chr5:41849000-41855200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:41849000-41856000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr5:41849000-41856200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:41849000-41856400	Strong transcription	Adipose Nuclei	Adipose
16	chr5:41849000-41856600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:41849000-41856600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:41849000-41857000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr5:41849000-41857000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:41849000-41857200	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:41849000-41857200	Strong transcription	K562	blood
22	chr5:41849000-41857800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:41849000-41862200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr5:41849000-41862600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:41849000-41862800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr5:41849000-41862800	Strong transcription	Fetal Thymus	thymus
27	chr5:41849200-41852400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:41849200-41852600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr5:41849200-41852800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr5:41849200-41852800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:41849200-41852800	Strong transcription	Brain Cingulate Gyrus	brain
32	chr5:41849200-41852800	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:41849200-41853000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:41849200-41853000	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr5:41849200-41853000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr5:41849200-41853000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:41849200-41853000	Strong transcription	Fetal Brain Female	brain
38	chr5:41849200-41853000	Strong transcription	Fetal Lung	lung
39	chr5:41849200-41853000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr5:41849200-41853000	Strong transcription	Fetal Muscle Leg	muscle
41	chr5:41849200-41853200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr5:41849200-41853400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr5:41849200-41853400	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr5:41849200-41853400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr5:41849200-41853400	Strong transcription	Thymus	Thymus
46	chr5:41849200-41853800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:41849200-41854000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:41849200-41854000	Strong transcription	Primary T cells from cord blood	blood
49	chr5:41849200-41854000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:41849200-41854000	Strong transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links