Variant report

Variant	rs2176415
Chromosome Location	chr2:63636568-63636569
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 155 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10168545	0.87[EUR][1000 genomes]
rs10170988	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10171223	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176522	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1023820	0.86[EUR][1000 genomes]
rs10469944	0.86[EUR][1000 genomes]
rs10469945	0.86[EUR][1000 genomes]
rs1082363	0.85[EUR][1000 genomes]
rs10865337	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10865338	0.88[EUR][1000 genomes]
rs10865339	0.86[EUR][1000 genomes]
rs11125967	0.80[EUR][1000 genomes]
rs11125977	0.84[EUR][1000 genomes]
rs11125978	0.85[EUR][1000 genomes]
rs112194	0.83[EUR][1000 genomes]
rs11693047	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11693909	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11883730	0.82[EUR][1000 genomes]
rs11894445	0.80[EUR][1000 genomes]
rs11898615	0.87[EUR][1000 genomes]
rs12105140	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1255	0.84[EUR][1000 genomes]
rs12618974	0.80[EUR][1000 genomes]
rs12713494	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713496	0.86[EUR][1000 genomes]
rs12990914	0.86[EUR][1000 genomes]
rs13011799	0.80[EUR][1000 genomes]
rs1356390	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446564	0.88[EUR][1000 genomes]
rs1446565	0.88[EUR][1000 genomes]
rs1446569	0.86[EUR][1000 genomes]
rs1550860	0.82[EUR][1000 genomes]
rs1568175	0.80[EUR][1000 genomes]
rs1607207	0.81[AFR][1000 genomes]
rs166384	0.85[EUR][1000 genomes]
rs174485	0.85[EUR][1000 genomes]
rs185499	0.83[EUR][1000 genomes]
rs1867847	0.85[EUR][1000 genomes]
rs1867849	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs187801	0.83[EUR][1000 genomes]
rs190519	0.80[EUR][1000 genomes]
rs1922421	0.80[EUR][1000 genomes]
rs196124	0.84[EUR][1000 genomes]
rs196125	0.83[EUR][1000 genomes]
rs2028883	0.85[EUR][1000 genomes]
rs2028887	0.87[EUR][1000 genomes]
rs2084200	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121350	0.85[EUR][1000 genomes]
rs2121351	0.85[EUR][1000 genomes]
rs2166494	0.85[EUR][1000 genomes]
rs2166497	0.86[EUR][1000 genomes]
rs2292793	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292794	0.80[EUR][1000 genomes]
rs2292795	0.80[EUR][1000 genomes]
rs2305157	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2421887	0.80[EUR][1000 genomes]
rs2422011	0.85[EUR][1000 genomes]
rs2604613	0.84[EUR][1000 genomes]
rs262470	0.85[EUR][1000 genomes]
rs262471	0.80[EUR][1000 genomes]
rs262472	0.84[EUR][1000 genomes]
rs262473	0.85[EUR][1000 genomes]
rs262474	0.82[EUR][1000 genomes]
rs262475	0.84[EUR][1000 genomes]
rs262476	0.84[EUR][1000 genomes]
rs262477	0.84[EUR][1000 genomes]
rs262478	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs262479	0.84[EUR][1000 genomes]
rs262480	0.83[EUR][1000 genomes]
rs262481	0.82[EUR][1000 genomes]
rs262482	0.83[EUR][1000 genomes]
rs262483	0.83[EUR][1000 genomes]
rs262484	0.83[EUR][1000 genomes]
rs262485	0.83[EUR][1000 genomes]
rs262487	0.83[EUR][1000 genomes]
rs262488	0.83[EUR][1000 genomes]
rs262489	0.80[EUR][1000 genomes]
rs262490	0.83[EUR][1000 genomes]
rs262493	0.85[EUR][1000 genomes]
rs262495	0.85[EUR][1000 genomes]
rs262501	0.85[EUR][1000 genomes]
rs262502	0.82[EUR][1000 genomes]
rs262503	0.84[EUR][1000 genomes]
rs262504	0.83[EUR][1000 genomes]
rs262505	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs262506	0.83[EUR][1000 genomes]
rs262515	0.83[AFR][1000 genomes]
rs2901580	0.80[EUR][1000 genomes]
rs2901614	0.83[EUR][1000 genomes]
rs3980466	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4255949	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4671065	0.86[EUR][1000 genomes]
rs4671067	0.83[EUR][1000 genomes]
rs4671068	0.86[EUR][1000 genomes]
rs4671069	0.84[EUR][1000 genomes]
rs4671487	0.85[AFR][1000 genomes]
rs4671494	0.82[EUR][1000 genomes]
rs4671503	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671505	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671508	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671509	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671512	0.84[EUR][1000 genomes]
rs4671514	0.84[EUR][1000 genomes]
rs4671515	0.86[EUR][1000 genomes]
rs4671516	0.85[EUR][1000 genomes]
rs4671517	0.82[EUR][1000 genomes]
rs4671519	0.84[EUR][1000 genomes]
rs6546001	0.80[EUR][1000 genomes]
rs6546002	0.82[EUR][1000 genomes]
rs6546004	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546005	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546007	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6546009	0.88[EUR][1000 genomes]
rs6546017	0.86[EUR][1000 genomes]
rs6546018	0.86[EUR][1000 genomes]
rs6546019	0.86[EUR][1000 genomes]
rs6706123	0.84[EUR][1000 genomes]
rs6708804	0.85[EUR][1000 genomes]
rs6717031	0.85[EUR][1000 genomes]
rs6724160	0.83[EUR][1000 genomes]
rs6732791	0.86[EUR][1000 genomes]
rs6734648	0.86[EUR][1000 genomes]
rs6736029	0.86[EUR][1000 genomes]
rs6736411	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738190	0.86[EUR][1000 genomes]
rs6754730	0.81[EUR][1000 genomes]
rs68183503	0.84[EUR][1000 genomes]
rs7558796	0.80[EUR][1000 genomes]
rs7563623	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7570031	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7571017	0.86[EUR][1000 genomes]
rs7571325	0.85[EUR][1000 genomes]
rs7571697	0.80[EUR][1000 genomes]
rs7576316	0.87[EUR][1000 genomes]
rs7577952	0.86[EUR][1000 genomes]
rs7584404	0.86[EUR][1000 genomes]
rs7599736	0.90[AFR][1000 genomes]
rs7606045	0.82[EUR][1000 genomes]
rs7607257	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7608470	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7608513	0.85[EUR][1000 genomes]
rs908621	0.80[EUR][1000 genomes]
rs932172	0.80[EUR][1000 genomes]
rs959195	0.86[EUR][1000 genomes]
rs964880	0.84[EUR][1000 genomes]
rs964903	0.88[EUR][1000 genomes]
rs9789351	0.88[EUR][1000 genomes]
rs989527	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv1800788	chr2:63473443-63900292	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv834241	chr2:63490262-63668205	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1002047	chr2:63584797-63648782	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv874234	chr2:63606001-63666590	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv874235	chr2:63622470-63709708	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3382119	chr2:63634350-63660437	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2176415	MDH1	cis	Adipose Subcutaneous	GTEx
rs2176415	WDPCP	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:63597800-63649200	Weak transcription	Fetal Lung	lung
2	chr2:63605000-63642400	Weak transcription	HSMMtube	muscle
3	chr2:63615600-63637000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:63615800-63637000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:63621400-63637000	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:63622200-63645400	Weak transcription	Liver	Liver
7	chr2:63624800-63642400	Weak transcription	Left Ventricle	heart
8	chr2:63626800-63644000	Weak transcription	Gastric	stomach
9	chr2:63627000-63637600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:63627600-63636600	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:63628200-63668200	Weak transcription	Fetal Kidney	kidney
12	chr2:63628600-63651600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:63629600-63644400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:63629800-63637400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:63631600-63644000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:63631600-63652200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:63631800-63637400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:63631800-63637400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:63631800-63641800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:63631800-63643200	Weak transcription	Dnd41	blood
21	chr2:63631800-63643800	Weak transcription	Pancreas	Pancrea
22	chr2:63631800-63645000	Weak transcription	Brain Substantia Nigra	brain
23	chr2:63631800-63652400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:63631800-63654600	Weak transcription	Primary T cells from cord blood	blood
25	chr2:63631800-63661600	Weak transcription	Ovary	ovary
26	chr2:63631800-63665600	Weak transcription	Primary B cells from cord blood	blood
27	chr2:63631800-63675800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:63631800-63677200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:63631800-63681200	Weak transcription	Aorta	Aorta
30	chr2:63631800-63688000	Weak transcription	Right Ventricle	heart
31	chr2:63632000-63665400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:63633000-63649200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:63634200-63665800	Weak transcription	Fetal Heart	heart
34	chr2:63634400-63652000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:63634600-63641800	Weak transcription	Adipose Nuclei	Adipose
36	chr2:63635800-63636600	Enhancers	H1 Cell Line	embryonic stem cell
37	chr2:63636000-63643800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:63636000-63651600	Weak transcription	Fetal Stomach	stomach
39	chr2:63636200-63636800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:63636200-63638400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links