Variant report

Variant	rs7569887
Chromosome Location	chr2:180096751-180096752
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10164707	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10164814	0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs10177122	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10177402	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10181291	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10181464	0.84[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10182477	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10185803	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10188759	0.84[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap]
rs10194420	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10196366	0.86[ASN][1000 genomes]
rs10204985	0.88[ASN][1000 genomes]
rs10209183	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10209887	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10439300	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs10930859	0.80[AMR][1000 genomes]
rs12105846	0.84[ASN][1000 genomes]
rs12617002	1.00[ASW][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12621023	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs12621115	0.94[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622075	1.00[ASW][hapmap];0.84[CEU][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.93[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12623243	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12693179	0.84[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12693181	0.81[ASN][1000 genomes]
rs12693183	0.81[ASN][1000 genomes]
rs12987285	0.94[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13020645	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13382185	0.94[ASW][hapmap];0.84[CEU][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs13384403	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13392996	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs13396340	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13414296	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417919	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs17454311	0.82[CHD][hapmap]
rs2007593	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2166534	0.84[YRI][hapmap]
rs28838656	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4894082	0.82[YRI][hapmap]
rs57098667	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6433770	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs67043078	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6731614	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6743412	0.94[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759983	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7601366	0.84[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7608745	0.94[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288025	0.88[CEU][hapmap]
rs9288026	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]

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	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	esv1798738	chr2:180084168-180100584	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7569887	SESTD1	cis	cerebellum	SCAN
rs7569887	SESTD1	Cis_1M	lymphoblastoid	RTeQTL
rs7569887	SESTD1	cis	parietal	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180067600-180097600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:180067600-180104600	Weak transcription	Fetal Kidney	kidney
3	chr2:180068000-180103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:180083800-180102200	Weak transcription	HMEC	breast
5	chr2:180087200-180097600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr2:180088800-180098400	Weak transcription	Spleen	Spleen
7	chr2:180089600-180115200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:180089800-180100200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:180089800-180100200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:180089800-180102000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:180090000-180098400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:180090000-180102000	Weak transcription	Fetal Muscle Leg	muscle
13	chr2:180090600-180102000	Weak transcription	Psoas Muscle	Psoas
14	chr2:180090600-180102400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:180091200-180102400	Weak transcription	Left Ventricle	heart
16	chr2:180091200-180104600	Weak transcription	Right Ventricle	heart
17	chr2:180091600-180098200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr2:180091600-180100400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:180091800-180100200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:180091800-180100600	Weak transcription	Brain Angular Gyrus	brain
21	chr2:180091800-180101800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:180091800-180102000	Weak transcription	Fetal Brain Male	brain
23	chr2:180091800-180102200	Weak transcription	Fetal Brain Female	brain
24	chr2:180091800-180102200	Weak transcription	Fetal Heart	heart
25	chr2:180091800-180102400	Weak transcription	Colon Smooth Muscle	Colon
26	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
27	chr2:180092000-180097600	Weak transcription	A549	lung
28	chr2:180092000-180102800	Weak transcription	Fetal Intestine Large	intestine
29	chr2:180092200-180097800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:180092200-180098400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:180092200-180100200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr2:180092200-180100400	Weak transcription	Brain Germinal Matrix	brain
33	chr2:180092200-180101800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:180092200-180102400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:180092600-180099400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:180092600-180099800	Weak transcription	Brain Substantia Nigra	brain
37	chr2:180092600-180100600	Weak transcription	Aorta	Aorta
38	chr2:180092800-180098200	Weak transcription	Lung	lung
39	chr2:180092800-180100200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:180092800-180100600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:180092800-180102000	Weak transcription	Right Atrium	heart
42	chr2:180092800-180102000	Weak transcription	NHLF	lung
43	chr2:180092800-180104600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:180092800-180112400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:180093000-180098400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:180093000-180098400	Weak transcription	Gastric	stomach
47	chr2:180093000-180098400	Weak transcription	Pancreas	Pancrea
48	chr2:180093000-180098800	Weak transcription	Ovary	ovary
49	chr2:180093000-180100200	Weak transcription	Adipose Nuclei	Adipose
50	chr2:180093000-180100200	Weak transcription	Brain Inferior Temporal Lobe	brain

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