Variant report

Variant	rs6970688
Chromosome Location	chr7:30617800-30617801
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10227133	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10232372	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10233132	0.81[ASN][1000 genomes]
rs10237725	0.85[EUR][1000 genomes]
rs10239660	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10243040	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10249885	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10265589	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10480088	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074373	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951271	0.83[ASN][1000 genomes]
rs1141114	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761080	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532057	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12533961	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13228758	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468402	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1558064	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16875282	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16875285	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009662	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214837	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2240401	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2267710	0.84[ASN][1000 genomes]
rs2270025	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2391870	0.81[EUR][1000 genomes]
rs3779250	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3807632	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722992	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4722999	0.86[ASN][1000 genomes]
rs6462211	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947982	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6970807	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9648369	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][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	nsv538811	chr7:30549595-31405593	Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1024458	chr7:30601877-30649659	Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3417912	chr7:30612318-30619224	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6970688	AC005154.6	cis	Adipose Subcutaneous	GTEx
rs6970688	AC005154.6	cis	Artery Tibial	GTEx
rs6970688	LOC401320	Cis_1M	lymphoblastoid	RTeQTL
rs6970688	AC005154.6	cis	Esophagus Mucosa	GTEx
rs6970688	AC005154.6	cis	Nerve Tibial	GTEx
rs6970688	LOC222159	Cis_1M	lymphoblastoid	RTeQTL
rs6970688	AC005154.6	cis	Skin Sun Exposed Lower leg	GTEx
rs6970688	AC005154.6	cis	lung	GTEx
rs6970688	AC005154.6	cis	Thyroid	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:30586600-30620400	Weak transcription	Fetal Thymus	thymus
2	chr7:30591200-30633400	Weak transcription	Psoas Muscle	Psoas
3	chr7:30597400-30633200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr7:30597600-30624400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:30598400-30623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:30601800-30633000	Weak transcription	Hela-S3	cervix
7	chr7:30603200-30621000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:30603200-30628400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:30604600-30617800	Weak transcription	Right Ventricle	heart
10	chr7:30604600-30624400	Weak transcription	Gastric	stomach
11	chr7:30605600-30628200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:30607000-30633400	Weak transcription	Fetal Kidney	kidney
13	chr7:30608200-30618400	Weak transcription	Brain Substantia Nigra	brain
14	chr7:30608600-30618000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr7:30609800-30621400	Weak transcription	K562	blood
16	chr7:30612000-30618600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr7:30612200-30618000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:30612200-30618800	Strong transcription	Placenta	Placenta
19	chr7:30612200-30625000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:30612200-30625600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:30612200-30627000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:30612800-30619000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr7:30612800-30628600	Weak transcription	Stomach Mucosa	stomach
24	chr7:30613000-30618800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:30613200-30619000	Strong transcription	Osteobl	bone
26	chr7:30613200-30619600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
27	chr7:30613600-30619200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr7:30613800-30619400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr7:30614000-30619400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr7:30614000-30620200	Weak transcription	Aorta	Aorta
31	chr7:30614000-30623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr7:30614000-30633200	Weak transcription	HUVEC	blood vessel
33	chr7:30614400-30619400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:30614400-30619400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr7:30614600-30617800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:30614600-30617800	Weak transcription	Colonic Mucosa	Colon
37	chr7:30615200-30618000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:30615200-30618600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
39	chr7:30615400-30619000	Strong transcription	Adipose Nuclei	Adipose
40	chr7:30615400-30619200	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr7:30615600-30633200	Weak transcription	Brain Germinal Matrix	brain
42	chr7:30615600-30633400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:30615800-30627000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr7:30616000-30622000	Strong transcription	A549	lung
45	chr7:30616000-30625400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:30616200-30618400	Strong transcription	Fetal Brain Male	brain
47	chr7:30616200-30618600	Strong transcription	HSMM	muscle
48	chr7:30616200-30618800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
49	chr7:30616200-30619400	ZNF genes & repeats	GM12878-XiMat	blood
50	chr7:30616200-30620800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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