Variant report

Variant	rs2286578
Chromosome Location	chr12:4835882-4835883
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10047570	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10083146	0.81[ASN][1000 genomes]
rs1009633	0.86[CHB][hapmap]
rs10160902	0.90[ASN][1000 genomes]
rs1024655	0.83[ASN][1000 genomes]
rs10431361	0.91[ASN][1000 genomes]
rs10431362	0.89[ASN][1000 genomes]
rs10774256	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs10774260	0.81[ASN][1000 genomes]
rs10774267	0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10849125	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10849126	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849128	0.89[ASN][1000 genomes]
rs10849129	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849130	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849133	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849137	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849138	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10849139	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10849143	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.95[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11063314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063318	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11063323	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11063327	0.94[ASN][1000 genomes]
rs11063328	0.93[ASN][1000 genomes]
rs11063331	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12296205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312983	0.82[CEU][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12320374	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12422704	0.82[CEU][hapmap]
rs1468556	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17783373	0.90[ASN][1000 genomes]
rs1990310	0.81[ASN][1000 genomes]
rs2109099	0.89[ASN][1000 genomes]
rs2109100	0.89[ASN][1000 genomes]
rs2159354	0.91[ASN][1000 genomes]
rs2159355	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2191157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240762	0.86[CHB][hapmap]
rs2267552	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs2286580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2286581	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2286582	0.86[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs2359466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2359467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35049745	0.90[ASN][1000 genomes]
rs3782740	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782742	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147696	0.81[ASN][1000 genomes]
rs4765779	0.90[ASN][1000 genomes]
rs4765780	0.87[ASN][1000 genomes]
rs4765781	0.89[ASN][1000 genomes]
rs4765782	0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4766272	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs4766276	0.90[ASN][1000 genomes]
rs4766278	0.90[ASN][1000 genomes]
rs4766279	0.90[ASN][1000 genomes]
rs4766280	0.90[ASN][1000 genomes]
rs4766281	0.90[ASN][1000 genomes]
rs4766282	1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs4766283	1.00[CHB][hapmap];0.84[JPT][hapmap];0.94[ASN][1000 genomes]
rs4766286	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6489558	0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs6489560	0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs6489565	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6489566	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6489567	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7132030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136583	0.83[ASN][1000 genomes]
rs7137040	0.90[ASN][1000 genomes]
rs7137660	0.90[ASN][1000 genomes]
rs7295230	0.94[ASN][1000 genomes]
rs7295251	0.94[ASN][1000 genomes]
rs7297290	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7305387	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7306235	0.90[ASN][1000 genomes]
rs7311475	0.90[ASN][1000 genomes]
rs7311675	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7311694	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7312119	0.90[ASN][1000 genomes]
rs7314849	0.94[ASN][1000 genomes]
rs7315211	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7316209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7953170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7953399	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7953482	0.94[ASN][1000 genomes]
rs7966628	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967117	0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7970126	0.90[ASN][1000 genomes]
rs7972019	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7972501	0.90[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7975978	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]
rs7976011	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7976219	0.85[ASN][1000 genomes]
rs929481	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9300304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1054218	chr12:4819576-4882667	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286578	SLC2A14	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4825800-4838200	Weak transcription	Gastric	stomach
2	chr12:4827400-4849600	Weak transcription	Fetal Brain Female	brain
3	chr12:4830400-4846400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:4831800-4838400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:4832000-4837800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:4832200-4849800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:4832400-4849400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:4832600-4851600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:4832800-4843800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:4833600-4837200	Strong transcription	Brain Germinal Matrix	brain
11	chr12:4834000-4870200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:4834200-4842400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:4834400-4840400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:4834600-4837000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:4835400-4836400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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