Variant report

Variant	rs56675463
Chromosome Location	chr7:66245900-66245901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1267816	1.00[AFR][1000 genomes]
rs1267817	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1267818	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1267819	1.00[AFR][1000 genomes]
rs1267820	1.00[AFR][1000 genomes]
rs12698542	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12698551	0.87[ASN][1000 genomes]
rs13228779	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13229468	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13232393	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13233569	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13235282	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13236129	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13237544	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13238478	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13238612	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13247442	0.80[ASN][1000 genomes]
rs1573944	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1618893	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1638731	0.91[AFR][1000 genomes]
rs1638734	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1796215	1.00[AFR][1000 genomes]
rs1796220	1.00[AFR][1000 genomes]
rs1796228	1.00[AFR][1000 genomes]
rs1880644	0.81[AFR][1000 genomes]
rs1882655	1.00[AFR][1000 genomes]
rs1922723	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2141924	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2178742	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2533287	0.81[EUR][1000 genomes]
rs2533288	0.95[AFR][1000 genomes]
rs2659903	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2659911	1.00[AFR][1000 genomes]
rs2659913	1.00[AFR][1000 genomes]
rs2707823	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2707826	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2707828	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2707830	1.00[AFR][1000 genomes]
rs2707831	1.00[AFR][1000 genomes]
rs2707832	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2707833	0.87[AFR][1000 genomes]
rs2707838	1.00[AFR][1000 genomes]
rs2707840	1.00[AFR][1000 genomes]
rs2707844	0.95[AFR][1000 genomes]
rs34162778	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34314366	0.81[AFR][1000 genomes]
rs34423980	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs34559676	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34785430	0.90[AFR][1000 genomes]
rs34816289	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs35043782	0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs35111158	0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs35315599	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35390465	0.84[ASN][1000 genomes]
rs35481333	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35508430	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35624856	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35676956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35821254	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs35851021	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36059333	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs3936	1.00[AFR][1000 genomes]
rs4457208	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs55849324	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs55889925	0.87[ASN][1000 genomes]
rs56006261	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56235846	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs59308022	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60201031	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60326618	1.00[AFR][1000 genomes]
rs6460312	1.00[AFR][1000 genomes]
rs66510832	0.96[ASN][1000 genomes]
rs66630579	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67319329	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs71535634	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs71535635	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs71563136	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73135918	0.81[AFR][1000 genomes]
rs869249	0.90[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs876743	0.90[AFR][1000 genomes];0.87[ASN][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	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
2	nsv888328	chr7:66173040-66327654	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv981512	chr7:66223352-66249901	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv888329	chr7:66234585-66376095	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs56675463	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs56675463	RP4-756H11.3	cis	lung	GTEx
rs56675463	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs56675463	GUSB	cis	Whole Blood	GTEx
rs56675463	VKORC1L1	cis	Whole Blood	GTEx
rs56675463	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs56675463	ASL	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66207000-66255200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:66231200-66246400	Weak transcription	Right Ventricle	heart
3	chr7:66231400-66255000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:66232600-66279800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:66234800-66275800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:66235200-66261400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:66235400-66255400	Weak transcription	Fetal Heart	heart
8	chr7:66236000-66259000	Strong transcription	NHDF-Ad	bronchial
9	chr7:66236800-66247800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:66236800-66265200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr7:66236800-66276800	Strong transcription	Dnd41	blood
12	chr7:66236800-66277000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr7:66236800-66278400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr7:66237200-66262400	Weak transcription	Fetal Brain Male	brain
15	chr7:66237200-66277600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:66238000-66246600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr7:66238000-66253800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr7:66238200-66246600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:66238200-66247600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:66238200-66248800	Strong transcription	Primary B cells from cord blood	blood
21	chr7:66238200-66252800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:66238200-66252800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:66238200-66276600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr7:66238400-66247000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr7:66238400-66247800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr7:66238400-66248200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr7:66238400-66252800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr7:66238400-66252800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:66238600-66249200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr7:66238600-66255200	Weak transcription	Stomach Mucosa	stomach
31	chr7:66238800-66246400	Strong transcription	Adipose Nuclei	Adipose
32	chr7:66239200-66246400	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr7:66239800-66246400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:66239800-66254800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:66240000-66246600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr7:66240400-66260000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr7:66241000-66254800	Weak transcription	A549	lung
38	chr7:66241400-66250200	Weak transcription	Brain Angular Gyrus	brain
39	chr7:66241600-66247000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr7:66241600-66247400	Weak transcription	Gastric	stomach
41	chr7:66241800-66249000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:66242000-66246400	Weak transcription	Lung	lung
43	chr7:66242000-66246400	Weak transcription	Pancreas	Pancrea
44	chr7:66242000-66246400	Weak transcription	Thymus	Thymus
45	chr7:66242000-66252000	Weak transcription	Ovary	ovary
46	chr7:66242000-66255200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr7:66242200-66246400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:66242200-66246400	Weak transcription	Brain Substantia Nigra	brain
49	chr7:66242200-66246600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr7:66242200-66250200	Weak transcription	H1 Cell Line	embryonic stem cell

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