Variant report

Variant	rs7865071
Chromosome Location	chr9:21890326-21890327
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10117507	0.90[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10811635	0.86[GIH][hapmap];0.87[TSI][hapmap]
rs10965165	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10965168	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10965174	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10965175	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11526324	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11531660	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11536713	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12236681	0.87[AMR][1000 genomes]
rs12236836	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12238536	0.88[AMR][1000 genomes]
rs12553901	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2027484	0.83[CEU][hapmap]
rs3802394	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4352938	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4587423	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4607709	0.83[CEU][hapmap]
rs4636295	0.80[GIH][hapmap]
rs4977569	1.00[CEU][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4977734	0.83[GIH][hapmap]
rs4977735	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4977736	0.95[CEU][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4977738	0.83[CEU][hapmap]
rs4977742	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4977743	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4977744	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4977745	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56213153	0.86[AMR][1000 genomes]
rs62556506	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62556519	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62556520	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6475592	0.83[CEU][hapmap]
rs7044807	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs756641	1.00[CEU][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv8426	chr9:21763810-22176200	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv892745	chr9:21857244-22006273	Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7865071	MTAP	cis	parietal	SCAN
rs7865071	MTAP	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:21859000-21892000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr9:21865400-21892600	Weak transcription	Colonic Mucosa	Colon
3	chr9:21873000-21893000	Weak transcription	NHDF-Ad	bronchial
4	chr9:21874400-21893800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:21880200-21890600	Weak transcription	HUVEC	blood vessel
6	chr9:21880400-21890800	Weak transcription	NH-A	brain
7	chr9:21880400-21892600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:21880400-21901400	Weak transcription	HSMMtube	muscle
9	chr9:21881400-21893200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:21881800-21890800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr9:21884200-21890800	Weak transcription	Right Ventricle	heart
12	chr9:21885400-21892200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:21886200-21891000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr9:21887000-21891000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:21887200-21890800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:21887200-21892800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr9:21887200-21919000	Weak transcription	Hela-S3	cervix
18	chr9:21887800-21892000	Weak transcription	Psoas Muscle	Psoas
19	chr9:21888200-21895600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:21888400-21890400	Weak transcription	Liver	Liver
21	chr9:21888400-21893000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:21888800-21891400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
23	chr9:21888800-21891400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
24	chr9:21889200-21890400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:21889400-21890800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:21889400-21891000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
27	chr9:21889400-21891000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr9:21889400-21891000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:21889400-21891400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:21889400-21891400	Strong transcription	Dnd41	blood
31	chr9:21889400-21891800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr9:21889400-21893800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:21889400-21894000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr9:21889600-21890800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:21889600-21891000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:21889600-21891000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr9:21889600-21891000	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:21889600-21891200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:21889600-21891200	ZNF genes & repeats	Aorta	Aorta
40	chr9:21889600-21891200	Strong transcription	Ovary	ovary
41	chr9:21889600-21891200	Strong transcription	NHEK	skin
42	chr9:21889600-21891400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
43	chr9:21889600-21891800	Strong transcription	Left Ventricle	heart
44	chr9:21889600-21893200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:21889800-21891200	Strong transcription	Primary B cells from peripheral blood	blood
46	chr9:21889800-21891400	ZNF genes & repeats	Fetal Intestine Large	intestine
47	chr9:21889800-21891400	ZNF genes & repeats	Fetal Lung	lung
48	chr9:21889800-21891800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:21889800-21893200	Weak transcription	HepG2	liver
50	chr9:21890000-21890800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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