Variant report

Variant	rs3740107
Chromosome Location	chr10:45923770-45923771
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45911283..45913624-chr10:45922069..45924597,2	K562	blood:
2	chr10:45916737..45919807-chr10:45921818..45926405,4	K562	blood:

Variant related genes	Relation type
ENSG00000012779	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10793618	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs10793621	0.81[EUR][1000 genomes]
rs1080264	0.86[CEU][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs11239558	0.86[EUR][1000 genomes]
rs11239559	0.88[EUR][1000 genomes]
rs11239564	0.88[EUR][1000 genomes]
rs11239565	0.86[EUR][1000 genomes]
rs11239567	0.86[EUR][1000 genomes]
rs11239570	0.86[EUR][1000 genomes]
rs11239577	0.81[EUR][1000 genomes]
rs12217545	0.86[EUR][1000 genomes]
rs1565096	0.98[EUR][1000 genomes]
rs1565097	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1982794	0.86[EUR][1000 genomes]
rs1982795	0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs1994426	0.87[EUR][1000 genomes]
rs4948673	0.87[EUR][1000 genomes]
rs4949003	0.86[CEU][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs7074524	0.81[CEU][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7095806	0.86[EUR][1000 genomes]
rs73289207	0.86[EUR][1000 genomes]
rs7900810	0.86[EUR][1000 genomes]
rs7900977	0.95[EUR][1000 genomes]
rs7918454	0.87[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895105	chr10:45636867-45928822	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3740107	ALOX5	cis	cerebellum	SCAN
rs3740107	ZFAND4	cis	Nerve Tibial	GTEx
rs3740107	AGAP4	cis	Whole Blood	GTEx
rs3740107	AGAP4	cis	Artery Tibial	GTEx
rs3740107	ANUBL1	cis	cerebellum	SCAN
rs3740107	AGAP4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45916600-45924400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:45916600-45949200	Weak transcription	Gastric	stomach
3	chr10:45917600-45924400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr10:45918000-45923800	Weak transcription	GM12878-XiMat	blood
5	chr10:45918600-45925800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr10:45918600-45929200	Strong transcription	Primary B cells from peripheral blood	blood
7	chr10:45920000-45925800	Enhancers	Pancreas	Pancrea
8	chr10:45921400-45923800	Strong transcription	Spleen	Spleen
9	chr10:45921400-45930800	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr10:45921400-45931600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr10:45921600-45925400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:45921600-45930400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr10:45921800-45925800	Strong transcription	Placenta	Placenta
14	chr10:45921800-45928600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr10:45921800-45933800	Weak transcription	Esophagus	oesophagus
16	chr10:45922000-45925000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr10:45922000-45928000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:45922000-45928800	Weak transcription	Thymus	Thymus
19	chr10:45922200-45925200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:45922200-45925200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr10:45922400-45925200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:45922800-45923800	Genic enhancers	Primary B cells from cord blood	blood
23	chr10:45922800-45924000	Bivalent Enhancer	Fetal Heart	heart
24	chr10:45923200-45923800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
25	chr10:45923200-45923800	Active TSS	Fetal Kidney	kidney
26	chr10:45923200-45923800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
27	chr10:45923200-45925000	ZNF genes & repeats	Lung	lung
28	chr10:45923400-45923800	Bivalent Enhancer	Adipose Nuclei	Adipose
29	chr10:45923400-45924000	Enhancers	H1 Cell Line	embryonic stem cell
30	chr10:45923400-45924000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:45923400-45924000	Bivalent/Poised TSS	Fetal Lung	lung
32	chr10:45923600-45924000	Bivalent Enhancer	Fetal Stomach	stomach
33	chr10:45923600-45924200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr10:45923600-45924200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr10:45923600-45924200	Enhancers	Right Ventricle	heart
36	chr10:45923600-45924800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr10:45923600-45924800	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr10:45923600-45925800	Enhancers	Fetal Thymus	thymus
39	chr10:45923600-45928000	Weak transcription	Right Atrium	heart
40	chr10:45923600-45928600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links