Variant report

Variant	rs11112213
Chromosome Location	chr12:105247010-105247011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10507189	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10778353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861283	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10861284	1.00[CEU][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861285	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861289	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10861290	1.00[CEU][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10861298	0.89[JPT][hapmap]
rs11112201	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112204	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11112211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112214	1.00[CEU][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112215	0.80[CEU][hapmap]
rs11112216	1.00[CEU][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112219	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11112222	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11112226	1.00[CEU][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11112236	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11112239	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11112240	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11112244	1.00[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11112247	1.00[CEU][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11112255	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11112262	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs11112267	0.82[AMR][1000 genomes]
rs11112272	0.89[CEU][hapmap];0.88[JPT][hapmap]
rs11112273	0.82[AMR][1000 genomes]
rs11112274	0.90[CEU][hapmap]
rs11112280	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs11112281	0.91[CEU][hapmap];0.88[JPT][hapmap]
rs11112288	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs11112289	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs11112290	0.91[CEU][hapmap]
rs11112304	0.91[CEU][hapmap]
rs11112344	0.89[JPT][hapmap]
rs12368247	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12368856	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12371663	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12372030	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs12372069	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16891	0.91[CEU][hapmap]
rs2047128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331189	0.89[CEU][hapmap]
rs4405400	0.83[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4603387	0.95[ASN][1000 genomes]
rs7303811	0.82[ASW][hapmap];0.91[CEU][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9669285	1.00[ASN][1000 genomes]

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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899497	chr12:105155291-105247010	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11112213	SLC41A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105220800-105260600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:105222000-105258400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:105222000-105258600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:105222200-105258800	Weak transcription	Pancreas	Pancrea
5	chr12:105229000-105259200	Weak transcription	Placenta	Placenta
6	chr12:105233200-105258600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:105236200-105258600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:105237400-105259000	Weak transcription	A549	lung
9	chr12:105238400-105257000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:105238400-105260400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr12:105238400-105280000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:105239800-105250400	Weak transcription	Adipose Nuclei	Adipose
13	chr12:105240600-105252400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:105240600-105258800	Weak transcription	Aorta	Aorta
15	chr12:105243000-105255800	Weak transcription	Colonic Mucosa	Colon
16	chr12:105243800-105265800	Weak transcription	Fetal Stomach	stomach
17	chr12:105244000-105248600	Weak transcription	Liver	Liver
18	chr12:105246400-105252600	Weak transcription	NHDF-Ad	bronchial
19	chr12:105247000-105252400	Weak transcription	Osteobl	bone

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