Variant report

Variant	rs2170503
Chromosome Location	chr12:40518341-40518342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	12:40517820-40521124..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs1031996	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10748014	0.90[JPT][hapmap]
rs10784370	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10784381	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10784386	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10878113	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10878222	0.85[JPT][hapmap]
rs1117378	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11175275	0.91[EUR][1000 genomes]
rs11175326	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175327	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11175656	0.90[JPT][hapmap]
rs12230710	0.84[EUR][1000 genomes]
rs1352876	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1388587	0.82[ASN][1000 genomes]
rs1388588	0.82[ASN][1000 genomes]
rs1388589	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1388590	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1388591	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1463719	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1463720	0.91[ASN][1000 genomes]
rs1472118	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1482284	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1482285	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1482287	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1482288	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491927	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491928	0.82[ASN][1000 genomes]
rs1491929	0.88[ASN][1000 genomes]
rs1491930	0.87[ASN][1000 genomes]
rs1491931	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1844921	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1844922	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1873611	0.84[ASN][1000 genomes]
rs1873612	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1873613	0.84[ASN][1000 genomes]
rs1905121	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1948380	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2131082	0.88[ASN][1000 genomes]
rs2131083	0.88[ASN][1000 genomes]
rs2201143	0.88[ASN][1000 genomes]
rs2220677	0.88[ASN][1000 genomes]
rs2248928	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2249010	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2249017	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2404573	0.93[CEU][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2638231	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638232	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2638245	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2638249	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638251	0.87[ASN][1000 genomes]
rs2638252	0.82[ASN][1000 genomes]
rs2638253	0.82[ASN][1000 genomes]
rs2638254	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638257	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638258	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638259	0.90[ASN][1000 genomes]
rs2638260	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638262	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638263	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638264	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638266	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638267	0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2708449	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2708464	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708466	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708467	0.88[ASN][1000 genomes]
rs2708470	0.88[ASN][1000 genomes]
rs2708472	0.88[ASN][1000 genomes]
rs2708473	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708474	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2708476	0.87[ASN][1000 genomes]
rs2708477	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2708479	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2708480	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708481	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2708482	0.82[ASN][1000 genomes]
rs2708485	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708487	0.82[ASN][1000 genomes]
rs2708488	0.87[ASN][1000 genomes]
rs2708489	0.82[ASN][1000 genomes]
rs2708491	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708492	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708493	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708494	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3812791	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4360759	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4363681	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6581514	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581519	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7132203	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs716231	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs722817	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs728622	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs728623	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs728624	0.82[ASN][1000 genomes]
rs729216	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7306140	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7310430	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878010	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs900253	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs937109	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs937110	0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs937111	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899028	chr12:40478652-40524180	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv899029	chr12:40478652-40536061	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv1836585	chr12:40492814-40540939	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	esv1839483	chr12:40492814-40540939	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1846566	chr12:40498683-40527395	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv1838306	chr12:40499495-40527395	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2170503	AC079630.2	cis	Esophagus Mucosa	GTEx
rs2170503	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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