Variant report

Variant	rs6788978
Chromosome Location	chr3:47442083-47442084
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47442062-47442301	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47434735..47437692-chr3:47441632..47443336,2	MCF-7	breast:
2	chr3:47423869..47425978-chr3:47441656..47444550,3	K562	blood:
3	chr3:47422123..47424705-chr3:47440996..47443292,2	K562	blood:
4	chr3:47439793..47442419-chr3:47454584..47456285,2	K562	blood:

Variant related genes	Relation type
PTPN23	TF binding region
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1024036	1.00[EUR][1000 genomes]
rs1038393	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs10865947	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1091068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11707272	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs12330516	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12631697	1.00[EUR][1000 genomes]
rs13077134	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs13323092	1.00[EUR][1000 genomes]
rs1531874	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1872165	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2170814	1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs28735306	1.00[EUR][1000 genomes]
rs295431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs448018	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858812	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858823	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858855	1.00[AMR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6442066	1.00[EUR][1000 genomes]
rs6442068	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs648226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6772449	1.00[EUR][1000 genomes]
rs6778673	1.00[EUR][1000 genomes]
rs6778687	1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6785538	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787210	1.00[EUR][1000 genomes]
rs6789730	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs7372780	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7612191	0.87[AMR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621853	0.87[AMR][1000 genomes]
rs7630154	1.00[EUR][1000 genomes]
rs7639121	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs807930	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs900688	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900689	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900690	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900694	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs924009	1.00[EUR][1000 genomes]
rs9823480	1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9826488	1.00[EUR][1000 genomes]
rs9828124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828473	1.00[EUR][1000 genomes]
rs9852167	1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]
rs9861265	1.00[EUR][1000 genomes]
rs9869489	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47423600-47446000	Weak transcription	Colonic Mucosa	Colon
2	chr3:47423800-47447400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:47423800-47448000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:47423800-47449800	Weak transcription	A549	lung
5	chr3:47424000-47446000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:47426200-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:47427600-47448400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:47428200-47449000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:47430200-47449600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:47431000-47448600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr3:47434000-47447400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:47436000-47446200	Strong transcription	Fetal Intestine Small	intestine
13	chr3:47436000-47454600	Weak transcription	Hela-S3	cervix
14	chr3:47436200-47462000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:47436400-47443600	Strong transcription	Dnd41	blood
16	chr3:47436400-47446000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:47436400-47446000	Strong transcription	Fetal Stomach	stomach
18	chr3:47436600-47446000	Weak transcription	Stomach Mucosa	stomach
19	chr3:47436600-47447800	Weak transcription	Small Intestine	intestine
20	chr3:47436600-47454800	Weak transcription	Fetal Kidney	kidney
21	chr3:47436800-47446200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:47436800-47447800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr3:47437000-47443600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr3:47437000-47444200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:47437000-47446000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:47437000-47448200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:47437000-47450000	Weak transcription	HUVEC	blood vessel
28	chr3:47437200-47446000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:47437200-47446000	Weak transcription	Gastric	stomach
30	chr3:47437400-47442200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:47437400-47443600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:47437400-47444200	Strong transcription	Placenta	Placenta
33	chr3:47437400-47446000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:47437600-47442200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr3:47437600-47442200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:47437600-47446000	Weak transcription	Pancreas	Pancrea
37	chr3:47437600-47453400	Weak transcription	Psoas Muscle	Psoas
38	chr3:47437800-47462800	Weak transcription	Fetal Brain Male	brain
39	chr3:47438000-47442400	Strong transcription	Fetal Brain Female	brain
40	chr3:47438200-47444000	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:47438400-47446000	Weak transcription	Aorta	Aorta
42	chr3:47438400-47446000	Weak transcription	K562	blood
43	chr3:47438400-47446200	Weak transcription	Esophagus	oesophagus
44	chr3:47438600-47445600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:47438800-47446200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr3:47439000-47446200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:47439000-47448000	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr3:47439000-47448800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:47439200-47449200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:47439200-47455000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links