Variant report

Variant	rs2289994
Chromosome Location	chr2:179977252-179977253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10084229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10084475	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10170430	0.82[EUR][1000 genomes]
rs10173710	0.86[AFR][1000 genomes]
rs10196577	0.83[EUR][1000 genomes]
rs10197425	0.89[CHD][hapmap]
rs10205477	0.85[ASN][1000 genomes]
rs10208593	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[YRI][hapmap]
rs10439300	0.92[CEU][hapmap];0.89[JPT][hapmap]
rs10803924	0.91[CEU][hapmap];0.88[JPT][hapmap]
rs10930855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10930856	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs10930857	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs12615736	0.97[AFR][1000 genomes]
rs12621023	0.89[JPT][hapmap];0.92[YRI][hapmap]
rs12693175	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12693178	0.81[LWK][hapmap];0.88[YRI][hapmap]
rs12997079	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs13021442	0.87[ASN][1000 genomes]
rs13022867	1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs13029576	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13396334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13403231	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13404037	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13420572	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363260	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17363267	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs17454311	1.00[ASW][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs1900338	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1968618	0.92[YRI][hapmap]
rs2289993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28763731	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs340320	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs340332	0.89[JPT][hapmap]
rs340334	0.89[JPT][hapmap]
rs34728717	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4894081	0.88[YRI][hapmap]
rs55750558	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56109193	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56181927	0.88[ASN][1000 genomes]
rs67028844	0.88[ASN][1000 genomes]
rs67312569	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9288025	0.89[JPT][hapmap];0.85[YRI][hapmap]

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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2289994	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs2289994	SESTD1	cis	cerebellum	SCAN
rs2289994	SESTD1	cis	parietal	SCAN
rs2289994	SESTD1	cis	multi-tissue	Pritchard
rs2289994	OSBPL6	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-179980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:179967800-179982400	Weak transcription	Fetal Brain Male	brain
3	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
4	chr2:179969400-179980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
7	chr2:179970800-179985800	Strong transcription	Primary B cells from cord blood	blood
8	chr2:179970800-179987000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:179971200-179977600	Strong transcription	Fetal Lung	lung
10	chr2:179971200-179977800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:179971400-179979200	Weak transcription	Ovary	ovary
12	chr2:179971600-179979400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:179971800-179978400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:179972200-179982400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:179972400-179977600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr2:179972400-179979800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:179972400-179982200	Strong transcription	Liver	Liver
22	chr2:179972400-179985400	Strong transcription	Stomach Smooth Muscle	stomach
23	chr2:179972400-179986800	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr2:179972400-179987400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr2:179972600-179977600	Strong transcription	Brain Germinal Matrix	brain
26	chr2:179972600-179979600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:179972600-179979800	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:179972600-179985200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:179972600-179985200	Weak transcription	Fetal Heart	heart
30	chr2:179972600-180001800	Weak transcription	NHEK	skin
31	chr2:179972800-179977600	Strong transcription	Fetal Muscle Leg	muscle
32	chr2:179972800-179979400	Weak transcription	Thymus	Thymus
33	chr2:179972800-179989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr2:179973000-179982400	Strong transcription	Fetal Muscle Trunk	muscle
36	chr2:179973000-179982600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:179973000-179985800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:179973000-179989200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
40	chr2:179973200-179977800	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:179973200-179979200	Weak transcription	Hela-S3	cervix
42	chr2:179973200-179979800	Weak transcription	Fetal Intestine Small	intestine
43	chr2:179973200-179980800	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr2:179973200-179982200	Weak transcription	Colonic Mucosa	Colon
45	chr2:179973200-179982200	Weak transcription	Stomach Mucosa	stomach
46	chr2:179973200-179986800	Strong transcription	Adipose Nuclei	Adipose
47	chr2:179973200-179987000	Weak transcription	Right Ventricle	heart
48	chr2:179973200-179987400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:179973200-179988400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:179973200-179988800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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