Variant report

Variant	rs12997314
Chromosome Location	chr2:180106919-180106920
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10170520	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10174774	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10186198	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10188759	0.84[TSI][hapmap]
rs10192426	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs10205390	0.83[JPT][hapmap]
rs10205999	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10209887	0.84[TSI][hapmap]
rs10439299	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930858	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1158872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11884516	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894870	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11898291	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12622075	0.84[TSI][hapmap]
rs13026497	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13382185	0.84[TSI][hapmap]
rs13383965	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13391602	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13418701	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1374378	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]
rs1446674	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs1907421	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1979053	0.81[EUR][1000 genomes]
rs2008989	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2008999	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes]
rs2044479	0.87[ASW][hapmap];0.93[LWK][hapmap];1.00[YRI][hapmap]
rs2289992	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]
rs2847	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs340331	0.82[GIH][hapmap]
rs4585064	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6433757	0.87[EUR][1000 genomes]
rs6433760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6433761	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433764	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6433769	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6707081	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6734121	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6736098	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742739	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6743405	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6756326	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7562730	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7579536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7585600	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7608882	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs9288022	0.82[EUR][1000 genomes]

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
rs12997314	SESTD1	cis	cerebellum	SCAN
rs12997314	SESTD1	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180089600-180115200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:180091800-180127200	Weak transcription	Fetal Lung	lung
3	chr2:180092800-180112400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:180093000-180107800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:180098600-180118600	Weak transcription	Pancreas	Pancrea
6	chr2:180101200-180112200	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr2:180101800-180107000	Enhancers	Brain Substantia Nigra	brain
8	chr2:180102800-180127800	Weak transcription	Psoas Muscle	Psoas
9	chr2:180103000-180112200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:180103200-180116000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr2:180104600-180112000	Weak transcription	Primary B cells from cord blood	blood
12	chr2:180104800-180108000	Enhancers	HepG2	liver
13	chr2:180104800-180109400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:180105000-180107200	Weak transcription	HMEC	breast
15	chr2:180105000-180108200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:180105200-180107200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:180105200-180109400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:180105200-180112200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:180105400-180109400	Weak transcription	Adipose Nuclei	Adipose
20	chr2:180105600-180112400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:180105600-180112400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:180105600-180116000	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:180105600-180120000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:180105800-180109800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:180105800-180112200	Weak transcription	Stomach Mucosa	stomach
26	chr2:180105800-180112200	Weak transcription	Hela-S3	cervix
27	chr2:180106200-180107000	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:180106200-180112000	Weak transcription	Brain Anterior Caudate	brain
29	chr2:180106200-180116400	Weak transcription	Small Intestine	intestine
30	chr2:180106600-180107000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr2:180106800-180107000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr2:180106800-180108800	Weak transcription	Primary B cells from peripheral blood	blood

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