Variant report

Variant	rs1374378
Chromosome Location	chr2:179984117-179984118
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	chr2:179983325..179985286-chr2:179986584..179988899,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10170520	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10174774	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs10186198	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10205390	0.83[ASW][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.88[YRI][hapmap]
rs10205999	0.83[AFR][1000 genomes]
rs10209887	0.84[TSI][hapmap]
rs10439299	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10930858	0.82[AFR][1000 genomes]
rs1158872	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs11884516	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11894870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11898291	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12622075	0.84[TSI][hapmap]
rs12997314	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13026497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13382185	0.84[TSI][hapmap]
rs13383965	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13391602	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13418701	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1374379	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1446674	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs1979053	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2008989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2008999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289992	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]
rs2847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs340331	0.82[GIH][hapmap]
rs4585064	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433757	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6433761	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6433764	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707081	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6734121	0.83[AFR][1000 genomes]
rs6736098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][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];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6757681	0.88[YRI][hapmap]
rs7579536	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7585600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7608882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[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];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873023	0.88[YRI][hapmap]
rs9288022	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][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
rs1374378	SESTD1	cis	parietal	SCAN
rs1374378	SESTD1	cis	cerebellum	SCAN
rs1374378	SESTD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

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	chr2:179970800-179985800	Strong transcription	Primary B cells from cord blood	blood
5	chr2:179970800-179987000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:179971600-179991400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:179971600-180012600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:179972000-180005200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:179972000-180005200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:179972400-179985400	Strong transcription	Stomach Smooth Muscle	stomach
11	chr2:179972400-179986800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr2:179972400-179987400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr2:179972600-179985200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr2:179972600-179985200	Weak transcription	Fetal Heart	heart
15	chr2:179972600-180001800	Weak transcription	NHEK	skin
16	chr2:179972800-179989800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:179972800-180014600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:179973000-179985800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:179973000-179989200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:179973000-180007200	Weak transcription	GM12878-XiMat	blood
21	chr2:179973200-179986800	Strong transcription	Adipose Nuclei	Adipose
22	chr2:179973200-179987000	Weak transcription	Right Ventricle	heart
23	chr2:179973200-179987400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:179973200-179988400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:179973200-179988800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:179973200-179989200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:179973200-179989400	Weak transcription	Primary T cells from cord blood	blood
28	chr2:179973400-179990000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:179973400-180004400	Weak transcription	Pancreas	Pancrea
30	chr2:179973400-180006800	Weak transcription	Small Intestine	intestine
31	chr2:179973400-180012600	Weak transcription	NHLF	lung
32	chr2:179973400-180030200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:179973800-179986800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:179974400-179994200	Strong transcription	HepG2	liver
35	chr2:179975800-180047600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:179976000-180004400	Weak transcription	Aorta	Aorta
37	chr2:179976600-179989800	Weak transcription	Gastric	stomach
38	chr2:179977200-179988000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:179977400-179987400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:179977400-179987800	Weak transcription	Brain Angular Gyrus	brain
41	chr2:179977400-179988400	Weak transcription	Brain Substantia Nigra	brain
42	chr2:179977400-180004400	Weak transcription	Lung	lung
43	chr2:179977400-180005000	Weak transcription	Fetal Kidney	kidney
44	chr2:179977400-180049000	Weak transcription	HSMMtube	muscle
45	chr2:179977600-179985400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr2:179977600-179986000	Weak transcription	NH-A	brain
47	chr2:179977600-179988600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:179977600-180002000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:179977800-179988600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:179978200-180014600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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