Variant report

Variant	rs2663659
Chromosome Location	chr2:210504524-210504525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10172200	0.87[JPT][hapmap]
rs10196314	0.87[JPT][hapmap]
rs10196600	0.87[JPT][hapmap]
rs10198751	0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs10206817	0.93[JPT][hapmap]
rs10490021	0.87[JPT][hapmap]
rs10932305	0.87[JPT][hapmap]
rs11692075	0.87[JPT][hapmap]
rs12613705	0.81[CHD][hapmap]
rs12614031	0.87[JPT][hapmap]
rs12615372	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12616589	0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12618080	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs12620654	0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12622979	0.97[ASN][1000 genomes]
rs12992342	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13385585	0.87[JPT][hapmap]
rs13419929	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs1396779	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1509465	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1509468	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1509469	0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1509470	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs16843329	0.85[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs16843351	0.93[JPT][hapmap]
rs16843354	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs16843360	0.87[CHD][hapmap];0.86[JPT][hapmap]
rs16843382	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs16843453	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs16843614	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs16843618	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs169636	0.91[CEU][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2048250	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2191910	0.87[JPT][hapmap]
rs2239552	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs2239553	0.87[JPT][hapmap]
rs2239672	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs2268042	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs2268044	0.87[JPT][hapmap]
rs2271252	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs2286849	0.86[JPT][hapmap]
rs2286850	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs2300154	0.87[JPT][hapmap]
rs2366112	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2663647	0.90[YRI][hapmap]
rs2663648	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2663649	0.85[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2663650	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2663651	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2663653	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2710474	0.98[ASN][1000 genomes]
rs2710475	0.99[ASN][1000 genomes]
rs2710477	0.91[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2710479	0.83[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2710480	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2710482	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs2710486	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs288070	0.91[CEU][hapmap]
rs288071	0.91[CEU][hapmap]
rs288079	0.91[CEU][hapmap];0.93[JPT][hapmap]
rs288081	0.91[CEU][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs288087	0.91[CEU][hapmap];0.93[JPT][hapmap]
rs288094	0.91[CEU][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap]
rs288096	0.91[CEU][hapmap]
rs34455059	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34850994	0.99[ASN][1000 genomes]
rs35409969	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3738935	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs3754597	0.87[JPT][hapmap]
rs3768810	0.87[JPT][hapmap]
rs3768813	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs3768814	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs3768815	0.87[JPT][hapmap]
rs3768816	0.87[JPT][hapmap]
rs3768822	0.87[JPT][hapmap]
rs3768826	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs3768832	0.87[JPT][hapmap]
rs3768833	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs3768834	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs3768835	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs3820746	0.91[JPT][hapmap]
rs3820748	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs4673486	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs55911510	0.95[ASN][1000 genomes]
rs56023260	0.85[ASN][1000 genomes]
rs56775639	1.00[ASN][1000 genomes]
rs56853570	0.98[ASN][1000 genomes]
rs57781584	0.89[ASN][1000 genomes]
rs58636345	0.96[ASN][1000 genomes]
rs59032380	1.00[ASN][1000 genomes]
rs60138527	0.89[ASN][1000 genomes]
rs60359169	0.97[ASN][1000 genomes]
rs60497472	0.89[ASN][1000 genomes]
rs6709925	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs6717554	0.87[JPT][hapmap]
rs6720659	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs6724834	0.87[JPT][hapmap]
rs6726061	0.91[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6733319	0.92[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6746029	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs723683	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs73071071	0.98[ASN][1000 genomes]
rs73071085	0.98[ASN][1000 genomes]
rs741006	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs741007	0.85[CHD][hapmap];0.86[JPT][hapmap]
rs7594601	0.85[CHD][hapmap];0.87[JPT][hapmap]
rs906831	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9288410	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs962475	0.85[CHB][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs994862	0.87[JPT][hapmap]

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	esv2754281	chr2:210484777-210543711	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2663659	LANCL1	cis	cerebellum	SCAN
rs2663659	C2orf67	cis	cerebellum	SCAN
rs2663659	GPR1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210494800-210517800	Weak transcription	Aorta	Aorta
2	chr2:210496200-210506800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:210496200-210507000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:210501000-210517800	Weak transcription	Fetal Brain Female	brain
5	chr2:210501200-210508000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:210501200-210516200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:210501800-210517800	Weak transcription	Brain Germinal Matrix	brain
8	chr2:210502800-210504600	Enhancers	NHEK	skin
9	chr2:210502800-210506000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:210502800-210506800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:210502800-210508000	Enhancers	HMEC	breast
12	chr2:210503000-210507400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:210503000-210508000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:210503000-210508400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:210503200-210506600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:210503200-210506800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:210503600-210505400	Weak transcription	NHDF-Ad	bronchial
18	chr2:210503600-210506800	Weak transcription	A549	lung
19	chr2:210503600-210517800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:210503800-210507000	Weak transcription	NH-A	brain
21	chr2:210504000-210506800	Weak transcription	HUVEC	blood vessel
22	chr2:210504000-210507000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr2:210504200-210504600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:210504200-210504800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:210504400-210505400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links