Variant report

Variant	rs7138860
Chromosome Location	chr12:51361463-51361464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11169679	0.82[AMR][1000 genomes]
rs12423207	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs150909	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs161044	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs161045	0.82[EUR][1000 genomes]
rs161046	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs161047	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs17125370	1.00[GIH][hapmap];0.93[TSI][hapmap]
rs17229232	1.00[GIH][hapmap];0.85[TSI][hapmap]
rs2046498	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs224564	0.86[EUR][1000 genomes]
rs224566	0.86[EUR][1000 genomes]
rs224569	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs224570	0.86[EUR][1000 genomes]
rs224573	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs224574	0.82[CEU][hapmap]
rs224578	0.82[EUR][1000 genomes]
rs224585	0.80[EUR][1000 genomes]
rs224590	0.82[EUR][1000 genomes]
rs224592	0.82[EUR][1000 genomes]
rs224593	0.82[EUR][1000 genomes]
rs2554858	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554859	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554861	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630353	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630358	0.92[EUR][1000 genomes]
rs2630362	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs2630366	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2630367	1.00[EUR][1000 genomes]
rs319930	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319938	1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319940	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319941	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319943	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs319944	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs364627	0.82[CEU][hapmap]
rs390424	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs394384	0.82[CEU][hapmap]
rs445520	0.82[EUR][1000 genomes]
rs4768959	1.00[MEX][hapmap]
rs55874852	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580779	0.82[CEU][hapmap]
rs6580780	0.82[CEU][hapmap]
rs706803	1.00[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs706804	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7971712	1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs7972608	1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs7974923	1.00[MEX][hapmap]
rs7975628	1.00[MEX][hapmap]
rs829016	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829021	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs853236	0.92[EUR][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1053466	chr12:51350285-51375969	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7138860	SLC11A2	cis	lymphoblastoid	seeQTL
rs7138860	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
2	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
3	chr12:51329600-51373600	Weak transcription	Left Ventricle	heart
4	chr12:51331400-51378400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:51331600-51373800	Weak transcription	Pancreas	Pancrea
6	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:51331800-51382000	Weak transcription	Ovary	ovary
8	chr12:51332600-51365000	Weak transcription	Fetal Brain Female	brain
9	chr12:51340000-51361800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:51341600-51378200	Weak transcription	Right Ventricle	heart
11	chr12:51341800-51372600	Weak transcription	Osteobl	bone
12	chr12:51341800-51383200	Weak transcription	Fetal Brain Male	brain
13	chr12:51342400-51373200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:51342800-51378400	Weak transcription	NHLF	lung
15	chr12:51343000-51366200	Weak transcription	Brain Germinal Matrix	brain
16	chr12:51343200-51361600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:51343600-51366200	Weak transcription	Gastric	stomach
18	chr12:51344000-51382000	Weak transcription	Esophagus	oesophagus
19	chr12:51344600-51381600	Weak transcription	Spleen	Spleen
20	chr12:51347200-51362000	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:51347200-51378000	Weak transcription	Brain Angular Gyrus	brain
22	chr12:51347400-51378000	Weak transcription	Brain Anterior Caudate	brain
23	chr12:51349200-51363600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr12:51350800-51380600	Weak transcription	Fetal Lung	lung
25	chr12:51351200-51365200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:51354200-51361800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:51354200-51363000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:51354200-51365200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:51354400-51365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:51354400-51365200	Weak transcription	Dnd41	blood
31	chr12:51354400-51383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr12:51354600-51364200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:51355200-51365200	Weak transcription	HSMM	muscle
34	chr12:51355600-51378000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:51355800-51361600	Weak transcription	Thymus	Thymus
36	chr12:51355800-51362000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:51355800-51366200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr12:51355800-51378000	Weak transcription	A549	lung
39	chr12:51356000-51361600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:51356000-51365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:51356000-51372600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr12:51356200-51362000	Weak transcription	HSMMtube	muscle
43	chr12:51357600-51378000	Weak transcription	Psoas Muscle	Psoas
44	chr12:51357800-51362400	Weak transcription	Fetal Intestine Large	intestine
45	chr12:51358200-51366200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:51358400-51361600	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr12:51358400-51365200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:51358800-51364400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:51358800-51377800	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:51359000-51361600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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