Variant report

Variant	rs12615736
Chromosome Location	chr2:179965608-179965609
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10084229	0.89[JPT][hapmap]
rs10084475	0.91[AFR][1000 genomes]
rs10164707	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs10164814	1.00[CEU][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes]
rs10173710	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10181464	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs10188759	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs10196366	0.92[EUR][1000 genomes]
rs10208593	0.89[JPT][hapmap];0.96[YRI][hapmap]
rs10209887	0.94[CEU][hapmap]
rs10930855	0.89[JPT][hapmap]
rs10930857	0.86[JPT][hapmap];0.89[YRI][hapmap]
rs1159257	1.00[CHB][hapmap]
rs12621023	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs12621115	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs12622075	0.94[CEU][hapmap]
rs12693175	0.89[JPT][hapmap]
rs12693178	0.88[YRI][hapmap]
rs12693179	0.95[CEU][hapmap];0.90[JPT][hapmap]
rs12987285	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs13029576	0.88[JPT][hapmap]
rs13382185	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs13396334	0.89[JPT][hapmap]
rs13403102	0.81[EUR][1000 genomes]
rs13404037	0.89[JPT][hapmap]
rs17363260	0.89[JPT][hapmap]
rs17454311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1900338	0.85[AFR][1000 genomes]
rs1968618	0.92[YRI][hapmap]
rs2289993	0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2289994	0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs2655153	0.87[EUR][1000 genomes]
rs340354	0.88[EUR][1000 genomes]
rs340355	0.88[EUR][1000 genomes]
rs34728717	0.92[AFR][1000 genomes]
rs4894081	0.88[YRI][hapmap]
rs56109193	0.92[AFR][1000 genomes]
rs67312569	0.95[AFR][1000 genomes]
rs6743412	0.84[CEU][hapmap]
rs6759983	0.83[CEU][hapmap]
rs7601366	0.95[CEU][hapmap];0.89[JPT][hapmap]
rs7608745	0.84[CEU][hapmap]
rs9288025	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9288026	0.95[CEU][hapmap]

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	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv875457	chr2:179775893-179966804	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875458	chr2:179780624-179966804	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv875465	chr2:179843612-179966804	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1004693	chr2:179933683-180265288	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12615736	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs12615736	SESTD1	cis	multi-tissue	Pritchard

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179961000-179966400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:179961000-179970800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr2:179961200-179971200	Weak transcription	Dnd41	blood
4	chr2:179961600-179972400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr2:179961600-179972800	Weak transcription	Spleen	Spleen
6	chr2:179961600-179974000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:179961800-179972600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:179962000-179972600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:179962000-179972800	Weak transcription	Fetal Thymus	thymus
10	chr2:179962400-179972600	Weak transcription	Left Ventricle	heart
11	chr2:179962800-179972400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:179963000-179970800	Weak transcription	Primary B cells from cord blood	blood
13	chr2:179964200-179969600	Weak transcription	HMEC	breast
14	chr2:179964600-179966200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:179964600-179967400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:179964800-179967800	Weak transcription	Adipose Nuclei	Adipose
17	chr2:179965000-179966600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:179965000-179967200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:179965200-179967400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:179965200-179969600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:179965200-179971400	Weak transcription	Brain Germinal Matrix	brain
22	chr2:179965400-179969200	Weak transcription	Osteobl	bone
23	chr2:179965400-179970800	Weak transcription	HUVEC	blood vessel
24	chr2:179965400-179971200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:179965600-179969800	Weak transcription	NHDF-Ad	bronchial

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