Variant report

Variant	rs3740110
Chromosome Location	chr10:45951424-45951425
allele	A/T
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	chr10:45946458-45953802	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45949197..45952104-chr10:45952176..45956457,4	K562	blood:
2	chr10:45949197..45952068-chr10:45954957..45956623,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OR13A1-4	chr10:45950066-45952578	NONHSAT013096

Variant related genes	Relation type
ENSG00000231964	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12765209	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12783037	0.86[CHB][hapmap]
rs17157784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17157883	1.00[ASN][1000 genomes]
rs2082109	0.86[ASN][1000 genomes]
rs2082110	0.86[ASN][1000 genomes]
rs2129644	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2306814	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3780902	0.81[ASN][1000 genomes]
rs3780904	0.90[ASN][1000 genomes]
rs3802547	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3824614	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs41426046	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs41519248	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59317220	0.90[ASN][1000 genomes]
rs73283191	0.81[ASN][1000 genomes]
rs73283196	0.81[ASN][1000 genomes]
rs74130824	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895107	chr10:45850300-45953767	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
5	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv895110	chr10:45912771-45953767	Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription 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	2 gene(s)	inside rSNPs	diseases
7	nsv1043536	chr10:45915941-46076235	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45929200-45951600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr10:45938600-45967200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:45938600-45967200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:45941800-45951600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr10:45942000-45951800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr10:45942800-45953200	Weak transcription	Spleen	Spleen
7	chr10:45943000-45952800	Weak transcription	Primary B cells from cord blood	blood
8	chr10:45943200-45955000	Weak transcription	Colonic Mucosa	Colon
9	chr10:45943200-45965400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr10:45943400-45954000	Weak transcription	K562	blood
11	chr10:45946200-45954400	Weak transcription	Fetal Brain Female	brain
12	chr10:45946800-45952600	Weak transcription	Fetal Lung	lung
13	chr10:45947200-45952200	Weak transcription	HepG2	liver
14	chr10:45947600-45951600	Weak transcription	Ovary	ovary
15	chr10:45947600-45952800	Weak transcription	Dnd41	blood
16	chr10:45947800-45953400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr10:45948000-45963600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr10:45948400-45952000	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr10:45948400-45955600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr10:45948600-45955600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:45948600-45959800	Strong transcription	Fetal Intestine Small	intestine
22	chr10:45948600-45959800	Strong transcription	Fetal Stomach	stomach
23	chr10:45948800-45951800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:45948800-45951800	Enhancers	GM12878-XiMat	blood
25	chr10:45948800-45952000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:45948800-45953800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:45949200-45965600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr10:45949400-45954400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr10:45949400-45955400	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr10:45949400-45959800	Strong transcription	Primary T cells from cord blood	blood
31	chr10:45949600-45952000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr10:45949800-45951600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:45949800-45951600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr10:45949800-45951600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr10:45949800-45953200	Weak transcription	Aorta	Aorta
36	chr10:45949800-45954200	Weak transcription	HSMMtube	muscle
37	chr10:45949800-45958600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:45950000-45951600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr10:45950000-45951600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr10:45950000-45951600	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr10:45950000-45951600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr10:45950000-45952600	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr10:45950000-45952800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr10:45950000-45956800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr10:45950000-45967200	Weak transcription	Psoas Muscle	Psoas
46	chr10:45950200-45952600	Strong transcription	Lung	lung
47	chr10:45950200-45952800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr10:45950200-45959400	Strong transcription	Fetal Intestine Large	intestine
49	chr10:45950200-45960600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr10:45950400-45951600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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