Variant report

Variant	rs1468348
Chromosome Location	chr7:38767914-38767915
allele	A/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	FOS	chr7:38767832-38768047	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr7:38767903-38768100	MCF10A-Er-Src	breast:	n/a	n/a
3	JUND	chr7:38767787-38768071	H1-hESC	embryonic stem cell:	n/a	n/a
4	JUND	chr7:38767810-38768103	HepG2	liver:	n/a	n/a
5	JUND	chr7:38767805-38768025	K562	blood:	n/a	n/a
6	JUND	chr7:38767838-38767970	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOSL2	chr7:38767716-38768121	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr7:38767910-38768256	K562	blood:	n/a	n/a
9	FOS	chr7:38767765-38768114	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr7:38767839-38768035	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38767860..38770728-chr7:38772914..38774538,2	MCF-7	breast:

Variant related genes	Relation type
VPS41	TF binding region

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1017028	0.86[ASN][1000 genomes]
rs10242048	0.86[ASN][1000 genomes]
rs10247503	0.90[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10251912	0.90[ASN][1000 genomes]
rs10254567	0.90[ASN][1000 genomes]
rs10271176	0.90[ASN][1000 genomes]
rs10486677	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs10486678	0.86[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11971020	0.88[ASN][1000 genomes]
rs11979618	0.99[ASN][1000 genomes]
rs11979824	0.88[ASN][1000 genomes]
rs11980882	0.80[JPT][hapmap]
rs12533557	0.90[ASN][1000 genomes]
rs12667567	0.86[ASN][1000 genomes]
rs12672237	0.97[ASN][1000 genomes]
rs12672750	0.99[ASN][1000 genomes]
rs12672793	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12672885	0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs12701652	0.80[JPT][hapmap]
rs12701659	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700072	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17700142	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs17700172	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700190	0.99[ASN][1000 genomes]
rs17700262	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17700392	0.88[ASN][1000 genomes]
rs17700752	0.86[CHD][hapmap]
rs17767695	0.95[ASN][1000 genomes]
rs17767770	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767818	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs17768153	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs17768212	0.88[ASN][1000 genomes]
rs17768753	0.80[JPT][hapmap]
rs1859494	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1859937	0.86[JPT][hapmap]
rs1864886	0.81[JPT][hapmap]
rs1978171	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1978172	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2074655	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2074657	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs2107743	0.90[ASN][1000 genomes]
rs2108507	0.80[JPT][hapmap]
rs2189855	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2214666	0.88[ASN][1000 genomes]
rs2240351	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2240352	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2240353	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2240354	0.87[ASN][1000 genomes]
rs2286082	0.88[ASN][1000 genomes]
rs2286084	0.88[ASN][1000 genomes]
rs2286086	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2286087	0.88[ASN][1000 genomes]
rs2286088	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2286091	0.88[ASN][1000 genomes]
rs2286094	0.88[ASN][1000 genomes]
rs2286098	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2286104	0.88[ASN][1000 genomes]
rs2286105	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2286106	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2286109	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2392598	0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs28548028	0.90[ASN][1000 genomes]
rs35253728	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35791079	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3735347	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3801139	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3801140	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3801141	0.88[ASN][1000 genomes]
rs3801143	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3801145	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs3801146	0.90[ASN][1000 genomes]
rs4723782	0.90[ASN][1000 genomes]
rs4723785	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs56050717	0.94[ASN][1000 genomes]
rs57091471	0.88[ASN][1000 genomes]
rs60590111	0.99[ASN][1000 genomes]
rs62444078	0.87[ASN][1000 genomes]
rs62444107	0.88[ASN][1000 genomes]
rs6462860	0.96[ASN][1000 genomes]
rs66662538	0.99[ASN][1000 genomes]
rs66796288	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66976998	0.94[ASN][1000 genomes]
rs67202646	0.96[ASN][1000 genomes]
rs733150	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs73368205	0.86[ASN][1000 genomes]
rs7778570	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7779329	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7780625	0.80[JPT][hapmap]
rs7783546	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7783695	0.86[JPT][hapmap]
rs7785911	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7786389	0.88[ASN][1000 genomes]
rs7794030	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7795874	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7797871	0.99[ASN][1000 genomes]
rs886646	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1468348	EEPD1	cis	parietal	SCAN
rs1468348	VPS41	cis	multi-tissue	Pritchard
rs1468348	EEPD1	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:38755800-38771600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:38757000-38784200	Weak transcription	HMEC	breast
5	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
6	chr7:38758600-38780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:38758800-38780000	Weak transcription	Brain Substantia Nigra	brain
8	chr7:38759000-38770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:38759200-38810200	Weak transcription	A549	lung
10	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr7:38759600-38779600	Weak transcription	Thymus	Thymus
12	chr7:38759600-38784200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:38759800-38768000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:38759800-38780600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:38760000-38773000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
17	chr7:38760600-38769800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:38760600-38770000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr7:38760800-38769800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
22	chr7:38761200-38785400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
24	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:38763400-38769800	Strong transcription	Adipose Nuclei	Adipose
26	chr7:38763400-38780400	Weak transcription	Fetal Kidney	kidney
27	chr7:38763400-38792600	Weak transcription	Small Intestine	intestine
28	chr7:38763400-38828800	Weak transcription	HepG2	liver
29	chr7:38763600-38772000	Strong transcription	Liver	Liver
30	chr7:38763800-38791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr7:38764000-38769000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:38764000-38769400	Strong transcription	Brain Anterior Caudate	brain
33	chr7:38764000-38769800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr7:38764000-38769800	Strong transcription	Fetal Intestine Small	intestine
35	chr7:38764200-38768600	Strong transcription	Brain Cingulate Gyrus	brain
36	chr7:38764200-38768800	Strong transcription	Fetal Muscle Trunk	muscle
37	chr7:38764200-38769400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr7:38764200-38769800	Strong transcription	Fetal Intestine Large	intestine
39	chr7:38764200-38769800	Strong transcription	Placenta	Placenta
40	chr7:38764200-38770000	Strong transcription	Fetal Stomach	stomach
41	chr7:38764200-38770000	Strong transcription	Gastric	stomach
42	chr7:38764200-38770200	Strong transcription	Primary B cells from cord blood	blood
43	chr7:38764200-38772000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr7:38764200-38772800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr7:38764400-38769600	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr7:38764400-38769800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:38764400-38769800	Strong transcription	Primary T cells from cord blood	blood
48	chr7:38764400-38770000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:38764400-38770000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:38764400-38770000	Strong transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links