Variant report

Variant	rs17700172
Chromosome Location	chr7:38764586-38764587
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

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];0.88[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]
rs1468348	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]
rs17700072	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17700142	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[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	0.88[CHD][hapmap]
rs17767695	0.95[ASN][1000 genomes]
rs17767770	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767818	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs17768153	0.86[CHB][hapmap];0.91[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];0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2074657	0.86[CHB][hapmap];0.88[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];0.91[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2240353	0.86[CHB][hapmap];0.91[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];0.91[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2286106	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2286109	0.95[CHB][hapmap];0.93[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];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[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];0.99[ASN][1000 genomes]
rs3801139	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3801140	0.91[CHB][hapmap];0.91[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3801141	0.88[ASN][1000 genomes]
rs3801143	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3801145	0.91[CHB][hapmap];0.95[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];0.93[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];0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17700172	EEPD1	cis	parietal	SCAN
rs17700172	VPS41	cis	parietal	SCAN
rs17700172	VPS41	Cis_1M	lymphoblastoid	RTeQTL
rs17700172	EEPD1	cis	cerebellum	SCAN

Chromatin state (count:119 , 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	chr7:38756400-38764600	Weak transcription	Fetal Brain Female	brain
5	chr7:38756800-38764800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:38757000-38784200	Weak transcription	HMEC	breast
7	chr7:38757200-38764600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:38757200-38764600	Weak transcription	Ovary	ovary
9	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
10	chr7:38757400-38764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:38758600-38764800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr7:38758600-38767000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr7:38758600-38767800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr7:38758600-38780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr7:38758800-38764800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr7:38758800-38765200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr7:38758800-38766400	Weak transcription	Brain Germinal Matrix	brain
18	chr7:38758800-38780000	Weak transcription	Brain Substantia Nigra	brain
19	chr7:38759000-38764600	Weak transcription	NHLF	lung
20	chr7:38759000-38770600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr7:38759200-38764800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:38759200-38810200	Weak transcription	A549	lung
23	chr7:38759400-38764600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:38759400-38764600	Weak transcription	Right Ventricle	heart
25	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr7:38759600-38764600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr7:38759600-38764800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:38759600-38779600	Weak transcription	Thymus	Thymus
29	chr7:38759600-38784200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:38759800-38764600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr7:38759800-38764600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr7:38759800-38765000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr7:38759800-38765000	Weak transcription	Fetal Lung	lung
34	chr7:38759800-38768000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr7:38759800-38780600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:38760000-38764600	Weak transcription	Colonic Mucosa	Colon
37	chr7:38760000-38773000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
39	chr7:38760400-38765200	Weak transcription	Colon Smooth Muscle	Colon
40	chr7:38760600-38769800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:38760600-38770000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr7:38760800-38769800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
45	chr7:38761200-38785400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr7:38761400-38764600	Weak transcription	Pancreas	Pancrea
47	chr7:38761600-38764600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr7:38761600-38764600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr7:38761600-38764600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr7:38761600-38764800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links