Variant report

Variant	rs2289992
Chromosome Location	chr2:179989039-179989040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10170520	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10174774	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10186198	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10188759	0.84[TSI][hapmap]
rs10192426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10205390	0.83[ASW][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.81[MKK][hapmap];0.88[YRI][hapmap]
rs10205999	0.82[AFR][1000 genomes]
rs10209887	0.84[TSI][hapmap]
rs10439299	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10930858	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1158872	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs11884516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11894870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs11898291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12622075	0.84[TSI][hapmap]
rs12997314	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13026497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13382185	0.84[TSI][hapmap]
rs13383965	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13391602	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13418701	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1374378	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1374379	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1446674	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1907421	0.81[EUR][1000 genomes]
rs1979053	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2008989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2008999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs340331	0.82[GIH][hapmap]
rs4585064	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433757	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433760	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6433761	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433764	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6707081	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6734121	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6736098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742739	0.81[EUR][1000 genomes]
rs6742744	0.82[YRI][hapmap]
rs6743405	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6756326	0.82[EUR][1000 genomes]
rs6757681	0.88[YRI][hapmap]
rs7562730	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7579536	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7585600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7608882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs873023	0.88[YRI][hapmap]
rs9288022	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2289992	SESTD1	cis	parietal	SCAN
rs2289992	SESTD1	cis	cerebellum	SCAN
rs2289992	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179967800-180004400	Weak transcription	Esophagus	oesophagus
2	chr2:179970000-180004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:179970200-179991000	Weak transcription	Psoas Muscle	Psoas
4	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:179972600-180001800	Weak transcription	NHEK	skin
9	chr2:179972800-179989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:179973000-179989200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
13	chr2:179973200-179989200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:179973200-179989400	Weak transcription	Primary T cells from cord blood	blood
15	chr2:179973400-179990000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:179973400-180004400	Weak transcription	Pancreas	Pancrea
17	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
18	chr2:179973400-180012600	Weak transcription	NHLF	lung
19	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:179974400-179994200	Strong transcription	HepG2	liver
21	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:179976000-180004400	Weak transcription	Aorta	Aorta
23	chr2:179976600-179989800	Weak transcription	Gastric	stomach
24	chr2:179977400-180004400	Weak transcription	Lung	lung
25	chr2:179977400-180005000	Weak transcription	Fetal Kidney	kidney
26	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
27	chr2:179977600-180002000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:179978800-180004400	Weak transcription	Spleen	Spleen
30	chr2:179980000-180038800	Weak transcription	HMEC	breast
31	chr2:179980000-180056800	Weak transcription	HSMM	muscle
32	chr2:179980400-179989400	Weak transcription	Thymus	Thymus
33	chr2:179980400-180005200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:179980400-180005600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr2:179980800-179989400	Weak transcription	Fetal Thymus	thymus
36	chr2:179981000-179991000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr2:179981200-179990200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:179981400-180001800	Weak transcription	Placenta	Placenta
39	chr2:179981400-180005000	Weak transcription	Ovary	ovary
40	chr2:179981400-180016800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:179981600-179991000	Weak transcription	Brain Anterior Caudate	brain
42	chr2:179981600-179997600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:179981600-180004400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:179981600-180005000	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:179981800-180005400	Weak transcription	Osteobl	bone
46	chr2:179982400-179989400	Weak transcription	NHDF-Ad	bronchial
47	chr2:179982400-180004400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:179982800-180004400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:179982800-180004600	Weak transcription	Fetal Brain Male	brain
50	chr2:179983600-180005000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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