Variant report

Variant	rs10878224
Chromosome Location	chr12:40614601-40614602
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40611277..40614132-chr12:40614284..40617171,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1031996	0.89[CHB][hapmap]
rs10748014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784381	0.89[CHB][hapmap]
rs10784386	0.89[CHB][hapmap]
rs10784428	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10878220	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10878222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175326	0.89[CHB][hapmap]
rs11175656	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12827541	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1352876	0.89[CHB][hapmap]
rs1388589	0.81[ASN][1000 genomes]
rs1463719	0.84[CHB][hapmap]
rs1472118	0.84[CHB][hapmap]
rs1491927	0.84[ASN][1000 genomes]
rs1491929	0.82[ASN][1000 genomes]
rs1491931	0.89[CHB][hapmap]
rs1602578	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1844921	0.86[ASN][1000 genomes]
rs1844922	0.86[ASN][1000 genomes]
rs1873612	0.83[ASN][1000 genomes]
rs1948380	0.84[ASN][1000 genomes]
rs2131082	0.82[ASN][1000 genomes]
rs2131083	0.82[ASN][1000 genomes]
rs2201143	0.82[ASN][1000 genomes]
rs2220677	0.82[ASN][1000 genomes]
rs2638245	0.89[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2638249	0.84[ASN][1000 genomes]
rs2638251	0.84[ASN][1000 genomes]
rs2638254	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2638257	0.83[ASN][1000 genomes]
rs2638258	0.83[ASN][1000 genomes]
rs2638260	0.89[CHB][hapmap]
rs2638263	0.89[CHB][hapmap]
rs2638264	0.84[CHB][hapmap]
rs2638266	0.89[CHB][hapmap]
rs2708464	0.81[ASN][1000 genomes]
rs2708466	0.81[ASN][1000 genomes]
rs2708467	0.82[ASN][1000 genomes]
rs2708470	0.82[ASN][1000 genomes]
rs2708472	0.82[ASN][1000 genomes]
rs2708473	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs2708474	0.83[ASN][1000 genomes]
rs2708476	0.84[ASN][1000 genomes]
rs2708480	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2708485	0.84[ASN][1000 genomes]
rs2708488	0.84[ASN][1000 genomes]
rs2708491	0.84[ASN][1000 genomes]
rs2708492	0.84[ASN][1000 genomes]
rs2708493	0.85[ASN][1000 genomes]
rs2708494	0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4360759	0.84[CHB][hapmap]
rs4363681	0.83[ASN][1000 genomes]
rs4767967	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768221	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs716231	0.89[CHB][hapmap];0.83[ASN][1000 genomes]
rs728622	0.84[ASN][1000 genomes]
rs728623	0.84[ASN][1000 genomes]
rs7306140	0.84[CHB][hapmap]
rs878010	0.84[CHB][hapmap]
rs900253	0.84[CHB][hapmap]
rs937109	0.89[CHB][hapmap]

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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	esv3432476	chr12:40614375-40614618	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10878224	AC079630.2	cis	Esophagus Mucosa	GTEx
rs10878224	SLC2A13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40610800-40616600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:40611000-40615600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:40611000-40618000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:40611200-40615600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr12:40611200-40617400	Weak transcription	A549	lung
6	chr12:40611400-40615200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:40611400-40615400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:40613600-40615600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr12:40614400-40615200	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr12:40614600-40615400	Enhancers	Primary B cells from cord blood	blood

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