Variant report

Variant	rs9288026
Chromosome Location	chr2:180103609-180103610
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	chr2:180099965..180101717-chr2:180103234..180105570,2	K562	blood:
2	chr2:180099014..180101971-chr2:180103448..180105283,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10164707	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10164814	0.95[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs10176829	0.82[AMR][1000 genomes]
rs10177122	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10177402	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10181291	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10181464	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10182477	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10185803	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10188759	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[EUR][1000 genomes]
rs10194420	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10194534	0.93[EUR][1000 genomes]
rs10196366	0.88[ASN][1000 genomes]
rs10204985	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10209183	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10209887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10439300	0.97[YRI][hapmap];0.98[AFR][1000 genomes]
rs10930859	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12105846	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12617002	1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12621023	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12621115	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12622075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12623243	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12693179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693181	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693183	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12987285	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13020645	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13382185	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13384403	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13392996	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13396340	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13414296	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13417919	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17454311	0.94[CEU][hapmap]
rs2007593	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28838656	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57098667	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433770	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67043078	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6731614	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6743412	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6759983	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7569887	0.83[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7601366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7608745	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9288025	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	nsv834471	chr2:179974303-180123027	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv834472	chr2:180091670-180220448	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9288026	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs9288026	SESTD1	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180067600-180104600	Weak transcription	Fetal Kidney	kidney
2	chr2:180068000-180103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:180089600-180115200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:180091200-180104600	Weak transcription	Right Ventricle	heart
5	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
6	chr2:180092800-180104600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:180092800-180112400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:180093000-180107800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:180095200-180104000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:180098000-180105200	Weak transcription	Fetal Thymus	thymus
11	chr2:180098600-180118600	Weak transcription	Pancreas	Pancrea
12	chr2:180099000-180103800	Weak transcription	Primary B cells from cord blood	blood
13	chr2:180100400-180104000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr2:180100400-180104200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr2:180100600-180103800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:180100600-180104000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr2:180100800-180104000	Weak transcription	NH-A	brain
18	chr2:180100800-180104400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:180100800-180104800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr2:180100800-180105000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:180100800-180105200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:180101200-180105200	Weak transcription	Aorta	Aorta
23	chr2:180101200-180112200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr2:180101800-180105000	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr2:180101800-180105600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:180101800-180107000	Enhancers	Brain Substantia Nigra	brain
27	chr2:180102000-180103800	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr2:180102000-180104200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr2:180102000-180104200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:180102000-180105000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:180102000-180105200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:180102000-180105400	Enhancers	Adipose Nuclei	Adipose
33	chr2:180102000-180105800	Enhancers	Brain Cingulate Gyrus	brain
34	chr2:180102200-180103800	Enhancers	Fetal Heart	heart
35	chr2:180102200-180104400	Enhancers	NHDF-Ad	bronchial
36	chr2:180102200-180104600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr2:180102200-180105000	Enhancers	HMEC	breast
38	chr2:180102200-180105800	Enhancers	HUVEC	blood vessel
39	chr2:180102400-180103800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:180102400-180104000	Weak transcription	HSMM	muscle
41	chr2:180102400-180105600	Enhancers	Colon Smooth Muscle	Colon
42	chr2:180102400-180106200	Enhancers	Brain Hippocampus Middle	brain
43	chr2:180102600-180104600	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:180102600-180105000	Enhancers	Primary T cells from cord blood	blood
45	chr2:180102600-180105200	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:180102800-180103800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr2:180102800-180104000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr2:180102800-180104000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:180102800-180104600	Weak transcription	Brain Angular Gyrus	brain
50	chr2:180102800-180104800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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