Variant report

Variant	rs2002825
Chromosome Location	chr5:68507635-68507636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs100192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940209	0.81[ASN][1000 genomes]
rs11742461	0.90[ASN][1000 genomes]
rs11744596	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745578	0.90[ASN][1000 genomes]
rs11748974	0.80[ASN][1000 genomes]
rs12659146	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13175606	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs151589	0.83[ASN][1000 genomes]
rs163442	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs163443	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs163444	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs164386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164388	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs164389	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs164715	0.83[ASN][1000 genomes]
rs1683831	0.92[ASN][1000 genomes]
rs184747	0.83[ASN][1000 genomes]
rs2130757	0.81[ASN][1000 genomes]
rs2171148	0.81[ASN][1000 genomes]
rs2172056	0.81[ASN][1000 genomes]
rs2242351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291519	0.81[ASN][1000 genomes]
rs2291520	0.81[ASN][1000 genomes]
rs239591	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2450230	0.84[ASN][1000 genomes]
rs2450246	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2637128	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2637129	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28506805	0.92[ASN][1000 genomes]
rs28576332	0.90[ASN][1000 genomes]
rs28693971	0.90[ASN][1000 genomes]
rs2913707	0.83[ASN][1000 genomes]
rs2930944	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930945	0.85[ASN][1000 genomes]
rs2930946	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2930949	0.81[ASN][1000 genomes]
rs2930951	0.81[ASN][1000 genomes]
rs2932770	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932771	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932772	0.85[ASN][1000 genomes]
rs2932773	0.85[ASN][1000 genomes]
rs2932775	0.85[ASN][1000 genomes]
rs2932776	0.85[ASN][1000 genomes]
rs2932777	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932778	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2932780	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2932782	0.80[ASN][1000 genomes]
rs2932783	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972358	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972361	0.81[ASN][1000 genomes]
rs2972366	0.81[ASN][1000 genomes]
rs2972373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972374	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972381	0.81[ASN][1000 genomes]
rs2972386	0.81[ASN][1000 genomes]
rs2972387	0.81[ASN][1000 genomes]
rs2972388	0.80[ASN][1000 genomes]
rs2972390	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34845020	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs350093	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs350094	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs350095	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350099	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350105	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs350107	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs350109	0.84[ASN][1000 genomes]
rs350115	0.83[ASN][1000 genomes]
rs350119	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350120	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs350123	0.85[ASN][1000 genomes]
rs350124	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs350125	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs351424	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs352626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353656	0.82[ASN][1000 genomes]
rs375285	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs376768	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs379434	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs386640	0.83[ASN][1000 genomes]
rs389686	0.88[ASW][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[ASN][1000 genomes]
rs389938	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390169	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs395122	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs419902	0.83[ASN][1000 genomes]
rs4266362	0.82[ASN][1000 genomes]
rs437665	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs444305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476125	0.92[ASN][1000 genomes]
rs4976159	0.91[ASN][1000 genomes]
rs4976188	0.91[ASN][1000 genomes]
rs648489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs651076	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs676879	0.81[ASN][1000 genomes]
rs6862253	0.89[ASN][1000 genomes]
rs693725	0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7719040	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2002825	CCDC125	cis	Muscle Skeletal	GTEx
rs2002825	MRPS36	cis	lymphoblastoid	seeQTL
rs2002825	CDK7	cis	Muscle Skeletal	GTEx
rs2002825	MRPS36	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68486000-68513600	Weak transcription	Gastric	stomach
2	chr5:68486200-68509400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr5:68486200-68509400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:68486200-68509400	Weak transcription	HSMM	muscle
5	chr5:68486200-68512800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr5:68486400-68512400	Weak transcription	Primary B cells from cord blood	blood
7	chr5:68486400-68512600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr5:68486400-68513000	Weak transcription	Brain Germinal Matrix	brain
9	chr5:68486400-68513000	Weak transcription	Fetal Intestine Large	intestine
10	chr5:68486400-68513000	Weak transcription	Osteobl	bone
11	chr5:68486600-68509200	Weak transcription	NHDF-Ad	bronchial
12	chr5:68487400-68508200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:68487400-68511200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:68487600-68508000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:68487600-68508000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:68487600-68508200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:68487600-68509000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:68490400-68513200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:68492400-68513000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr5:68492800-68512200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr5:68492800-68513000	Weak transcription	Fetal Brain Female	brain
22	chr5:68494200-68509400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:68494600-68513200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:68495000-68509400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr5:68495400-68512800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:68495400-68513000	Weak transcription	HMEC	breast
27	chr5:68495400-68513400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:68495600-68509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:68495600-68512400	Weak transcription	Primary T cells from cord blood	blood
30	chr5:68495600-68512600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:68495600-68512800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr5:68495600-68513000	Weak transcription	Fetal Lung	lung
33	chr5:68495600-68513200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:68495600-68513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:68497800-68513200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr5:68498000-68512800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr5:68498800-68508200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:68498800-68509400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:68500600-68513000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:68501600-68513000	Weak transcription	Thymus	Thymus
41	chr5:68502200-68509600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:68502800-68513600	Weak transcription	Small Intestine	intestine
43	chr5:68503000-68509200	Weak transcription	HepG2	liver
44	chr5:68503000-68509400	Weak transcription	A549	lung
45	chr5:68503000-68509400	Weak transcription	Hela-S3	cervix
46	chr5:68503000-68509400	Weak transcription	NHLF	lung
47	chr5:68503200-68509400	Weak transcription	NHEK	skin
48	chr5:68503800-68508000	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr5:68503800-68508000	Strong transcription	Dnd41	blood
50	chr5:68504200-68509000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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