Variant report

Variant	rs1565097
Chromosome Location	chr10:45924256-45924257
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	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: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10793618	0.90[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10793621	0.83[CHD][hapmap];0.80[EUR][1000 genomes]
rs1080264	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10900227	0.81[CEU][hapmap]
rs11239558	0.85[EUR][1000 genomes]
rs11239559	0.87[EUR][1000 genomes]
rs11239564	0.87[EUR][1000 genomes]
rs11239565	0.85[EUR][1000 genomes]
rs11239567	0.92[CHB][hapmap];0.85[EUR][1000 genomes]
rs11239570	0.85[EUR][1000 genomes]
rs11239577	0.80[EUR][1000 genomes]
rs12217545	0.84[EUR][1000 genomes]
rs1565096	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1982794	0.92[CHB][hapmap];0.85[EUR][1000 genomes]
rs1982795	0.81[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1994426	0.85[EUR][1000 genomes]
rs2279435	0.80[ASN][1000 genomes]
rs3740107	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4948673	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4949003	0.90[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7074524	0.86[CEU][hapmap];0.92[CHB][hapmap];0.86[CHD][hapmap];0.82[TSI][hapmap]
rs7095806	0.85[EUR][1000 genomes]
rs73289207	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7900810	0.85[EUR][1000 genomes]
rs7900977	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7918454	0.81[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.84[TSI][hapmap];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1565097	AGAP4	cis	Skin Sun Exposed Lower leg	GTEx
rs1565097	AGAP4	cis	Whole Blood	GTEx
rs1565097	AGAP4	cis	Artery Tibial	GTEx

Chromatin state (count:33 , 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	chr10:45918600-45925800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:45918600-45929200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr10:45920000-45925800	Enhancers	Pancreas	Pancrea
7	chr10:45921400-45930800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr10:45921400-45931600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr10:45921600-45925400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr10:45921600-45930400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr10:45921800-45925800	Strong transcription	Placenta	Placenta
12	chr10:45921800-45928600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr10:45921800-45933800	Weak transcription	Esophagus	oesophagus
14	chr10:45922000-45925000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:45922000-45928000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr10:45922000-45928800	Weak transcription	Thymus	Thymus
17	chr10:45922200-45925200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:45922200-45925200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr10:45922400-45925200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:45923200-45925000	ZNF genes & repeats	Lung	lung
21	chr10:45923600-45924800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr10:45923600-45924800	Bivalent Enhancer	Fetal Muscle Leg	muscle
23	chr10:45923600-45925800	Enhancers	Fetal Thymus	thymus
24	chr10:45923600-45928000	Weak transcription	Right Atrium	heart
25	chr10:45923600-45928600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr10:45923800-45924600	Genic enhancers	Spleen	Spleen
27	chr10:45923800-45925800	Strong transcription	GM12878-XiMat	blood
28	chr10:45923800-45926400	Strong transcription	Primary B cells from cord blood	blood
29	chr10:45924000-45928400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr10:45924000-45928600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:45924200-45924800	Bivalent Enhancer	Right Ventricle	heart
32	chr10:45924200-45925000	Strong transcription	Fetal Intestine Small	intestine
33	chr10:45924200-45928400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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