Variant report

Variant	rs12227244
Chromosome Location	chr12:60106164-60106165
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10431557	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10506398	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10506399	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs10877338	0.90[CHB][hapmap]
rs11173126	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs11173133	0.83[CEU][hapmap]
rs11173134	0.82[AFR][1000 genomes]
rs11173159	0.91[CEU][hapmap];0.81[CHB][hapmap]
rs12227270	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231311	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12231693	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs12231740	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12232002	0.82[CEU][hapmap];0.91[CHB][hapmap];0.83[AFR][1000 genomes]
rs12816935	0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17649424	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs17650311	0.86[CEU][hapmap];0.90[CHB][hapmap]
rs1795884	0.85[CHB][hapmap]
rs1795896	0.90[CHB][hapmap]
rs2706306	0.90[CHB][hapmap]
rs2706309	0.90[CHB][hapmap]
rs2706319	0.90[CHB][hapmap]
rs2711655	0.91[CHB][hapmap]
rs2711656	0.90[CHB][hapmap]
rs2711659	0.85[CHB][hapmap]
rs2711668	0.90[CHB][hapmap]
rs3763980	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs3847655	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61174819	0.81[EUR][1000 genomes]
rs7133415	0.86[CEU][hapmap];0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7136019	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7303876	0.91[CEU][hapmap];0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs995342	0.80[CHB][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2829972	chr12:60079404-60111653	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv899132	chr12:60087572-60211476	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12227244	SLC16A7	cis	multi-tissue	Pritchard
rs12227244	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60069600-60131400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr12:60086200-60106400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:60087600-60108000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:60089400-60126000	Weak transcription	Left Ventricle	heart
5	chr12:60093800-60107400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr12:60093800-60108800	Weak transcription	Ovary	ovary
7	chr12:60093800-60109800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:60093800-60126600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:60094000-60127200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:60094200-60107200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:60094200-60127200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:60095400-60114400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:60097200-60109600	Weak transcription	Dnd41	blood
14	chr12:60098000-60117000	Weak transcription	Psoas Muscle	Psoas
15	chr12:60098600-60109000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:60099200-60107600	Weak transcription	Hela-S3	cervix
17	chr12:60099200-60109200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:60099200-60126600	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr12:60099400-60130400	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:60099600-60143200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:60100000-60175200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr12:60100400-60126400	Weak transcription	Primary B cells from cord blood	blood
23	chr12:60100600-60127200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:60101600-60108800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:60101800-60122000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:60102400-60109400	Strong transcription	Primary T cells from cord blood	blood
27	chr12:60102600-60111000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:60103400-60111600	Weak transcription	GM12878-XiMat	blood
29	chr12:60104200-60138000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:60105000-60111600	Weak transcription	Thymus	Thymus
31	chr12:60105000-60112200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:60105200-60109200	Weak transcription	Pancreas	Pancrea
33	chr12:60105400-60106400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:60105400-60111000	Weak transcription	Adipose Nuclei	Adipose
35	chr12:60105400-60111200	Weak transcription	Fetal Thymus	thymus
36	chr12:60105600-60110400	Weak transcription	Aorta	Aorta
37	chr12:60105600-60129200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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