Variant report

Variant	rs2659913
Chromosome Location	chr7:66157336-66157337
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66150663..66153524-chr7:66155047..66157975,3	K562	blood:
2	chr7:66151342..66153524-chr7:66155047..66159440,3	K562	blood:
3	chr7:66155376..66157411-chr7:66204000..66206199,2	K562	blood:

Variant related genes	Relation type
ENSG00000243335	Chromatin interaction
ENSG00000272831	Chromatin interaction
ENSG00000154710	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1267816	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1267817	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1267819	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1267820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12698542	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13222887	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13224048	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13228779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs13229468	0.90[AFR][1000 genomes]
rs13232193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13235282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs13236129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13237037	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13237344	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13237544	0.91[AFR][1000 genomes]
rs13238612	0.86[AFR][1000 genomes]
rs13241548	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13247442	0.92[ASN][1000 genomes]
rs1573944	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1618893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1638731	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1638734	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1638736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1796215	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1796220	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796228	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796229	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1882655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922723	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2141924	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2178742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2533287	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2533288	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659903	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707823	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2707826	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2707828	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2707830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2707831	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2707832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707833	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2707844	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34162778	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34423980	0.90[AFR][1000 genomes]
rs34559676	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34807232	1.00[AFR][1000 genomes]
rs35261784	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35315599	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35370033	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35481333	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35508430	0.90[AFR][1000 genomes]
rs35624856	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35676956	1.00[AFR][1000 genomes]
rs35821254	0.90[AFR][1000 genomes]
rs35823062	1.00[AFR][1000 genomes]
rs35825036	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35851021	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs36059333	0.90[AFR][1000 genomes]
rs36104268	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3800822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4457208	0.90[AFR][1000 genomes]
rs55849324	0.87[AFR][1000 genomes]
rs56006261	0.90[AFR][1000 genomes]
rs56235846	0.85[AFR][1000 genomes]
rs56675463	1.00[AFR][1000 genomes]
rs58668827	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs58669269	0.91[AFR][1000 genomes]
rs59308022	0.91[AFR][1000 genomes]
rs60201031	1.00[AFR][1000 genomes]
rs60326618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6460312	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66630579	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71535635	0.95[AFR][1000 genomes]
rs71563118	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71563136	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73135918	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs876743	0.90[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	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
3	esv3385090	chr7:66146376-66205022	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3401338	chr7:66147493-66206298	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv970870	chr7:66147890-66158166	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2659913	RP4-756H11.3	cis	lung	GTEx
rs2659913	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs2659913	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL
rs2659913	GUSB	cis	Whole Blood	GTEx
rs2659913	ASL	cis	multi-tissue	Pritchard
rs2659913	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs2659913	VKORC1L1	cis	Whole Blood	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66148000-66157400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:66148000-66161800	Weak transcription	Left Ventricle	heart
3	chr7:66148000-66161800	Weak transcription	Right Atrium	heart
4	chr7:66148000-66165600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:66148000-66177600	Weak transcription	Aorta	Aorta
6	chr7:66148200-66157800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:66148200-66157800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:66148200-66157800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr7:66148200-66158400	Weak transcription	Primary T cells from cord blood	blood
10	chr7:66148200-66161800	Weak transcription	Psoas Muscle	Psoas
11	chr7:66148200-66162000	Weak transcription	Gastric	stomach
12	chr7:66148200-66162000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:66148200-66175600	Weak transcription	Primary B cells from cord blood	blood
14	chr7:66148400-66157400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:66148400-66157400	Weak transcription	Esophagus	oesophagus
16	chr7:66148400-66157400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr7:66148400-66157800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:66148400-66159000	Weak transcription	Placenta	Placenta
19	chr7:66148400-66159000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr7:66148400-66159200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr7:66148400-66161600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:66148400-66161600	Weak transcription	Brain Substantia Nigra	brain
23	chr7:66148400-66161800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:66148400-66161800	Weak transcription	Colon Smooth Muscle	Colon
25	chr7:66148400-66178400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:66148400-66182400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr7:66148400-66184400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr7:66148400-66184800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr7:66148600-66157800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr7:66148600-66157800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr7:66148600-66157800	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr7:66148600-66158600	Weak transcription	HSMMtube	muscle
33	chr7:66148600-66161800	Weak transcription	Brain Angular Gyrus	brain
34	chr7:66148600-66161800	Weak transcription	NH-A	brain
35	chr7:66148600-66172400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr7:66148600-66177400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr7:66149000-66157600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr7:66149000-66177600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:66149000-66199600	Weak transcription	Thymus	Thymus
40	chr7:66149200-66157400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:66149200-66159000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr7:66149200-66161800	Weak transcription	Brain Hippocampus Middle	brain
43	chr7:66149400-66157400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:66149400-66157400	Weak transcription	Lung	lung
45	chr7:66149400-66157800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr7:66149600-66158000	Weak transcription	Osteobl	bone
47	chr7:66149600-66159000	Weak transcription	Liver	Liver
48	chr7:66149600-66161800	Weak transcription	Adipose Nuclei	Adipose
49	chr7:66149600-66161800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr7:66149600-66178400	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links