Variant report

Variant	rs16840898
Chromosome Location	chr2:209174188-209174189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs10171006	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173938	0.91[ASN][1000 genomes]
rs10175739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs10176626	0.94[ASN][1000 genomes]
rs10182087	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10186531	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10189031	0.94[ASN][1000 genomes]
rs10197958	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10201702	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10208004	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10208191	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10208295	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs10210393	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1057390	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10804168	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932256	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932259	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932260	0.94[ASN][1000 genomes]
rs11677618	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11691208	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11691313	1.00[ASN][1000 genomes]
rs11695873	1.00[EUR][1000 genomes]
rs11897897	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12185547	1.00[EUR][1000 genomes]
rs12465862	1.00[EUR][1000 genomes]
rs12478198	1.00[EUR][1000 genomes]
rs12479282	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12617521	1.00[EUR][1000 genomes]
rs12618837	1.00[EUR][1000 genomes]
rs12621871	1.00[EUR][1000 genomes]
rs12623816	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12694105	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12694109	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs13392540	0.86[CHB][hapmap]
rs1370370	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370375	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1370377	1.00[JPT][hapmap]
rs1437414	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1446320	1.00[EUR][1000 genomes]
rs1446321	1.00[EUR][1000 genomes]
rs1465803	1.00[EUR][1000 genomes]
rs1465804	1.00[EUR][1000 genomes]
rs1469941	0.85[AFR][1000 genomes]
rs1529979	1.00[EUR][1000 genomes]
rs1561240	1.00[EUR][1000 genomes]
rs1584200	0.91[ASN][1000 genomes]
rs1595329	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16840798	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.87[YRI][hapmap]
rs16840864	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16840910	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16840936	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841092	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.87[YRI][hapmap]
rs16841231	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs16841233	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs16841234	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16841242	0.88[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.82[LWK][hapmap];0.86[MKK][hapmap]
rs1838794	1.00[EUR][1000 genomes]
rs1838795	1.00[EUR][1000 genomes]
rs1838796	1.00[EUR][1000 genomes]
rs1866044	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1866045	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs1898436	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1900239	0.94[ASN][1000 genomes]
rs2028146	1.00[EUR][1000 genomes]
rs2043720	1.00[EUR][1000 genomes]
rs2044457	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2118296	1.00[EUR][1000 genomes]
rs2118297	1.00[EUR][1000 genomes]
rs2196604	0.91[ASN][1000 genomes]
rs2304544	1.00[EUR][1000 genomes]
rs2363463	1.00[EUR][1000 genomes]
rs2363465	0.85[ASN][1000 genomes]
rs2363466	0.91[ASN][1000 genomes]
rs2363468	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2363469	1.00[EUR][1000 genomes]
rs2363579	1.00[EUR][1000 genomes]
rs2885785	1.00[EUR][1000 genomes]
rs2885786	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3856350	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4462735	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4673385	1.00[EUR][1000 genomes]
rs4673386	1.00[EUR][1000 genomes]
rs4673390	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4673391	0.91[ASN][1000 genomes]
rs4673392	0.91[ASN][1000 genomes]
rs4673393	0.94[ASN][1000 genomes]
rs4673395	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675745	1.00[EUR][1000 genomes]
rs4675747	1.00[EUR][1000 genomes]
rs4675748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4675750	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4675751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4675754	1.00[EUR][1000 genomes]
rs4675755	1.00[EUR][1000 genomes]
rs57553077	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57797425	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59149007	0.84[AFR][1000 genomes]
rs60446438	0.90[ASN][1000 genomes]
rs6435436	1.00[EUR][1000 genomes]
rs6435437	1.00[EUR][1000 genomes]
rs6435441	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435443	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435444	1.00[EUR][1000 genomes]
rs6435445	1.00[EUR][1000 genomes]
rs6435446	1.00[EUR][1000 genomes]
rs6435450	1.00[EUR][1000 genomes]
rs6705163	1.00[EUR][1000 genomes]
rs6708926	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711933	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713477	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs6718402	1.00[EUR][1000 genomes]
rs6721780	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6724208	0.94[ASN][1000 genomes]
rs6725932	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6733607	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734963	1.00[EUR][1000 genomes]
rs6736599	0.94[ASN][1000 genomes]
rs6742461	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751982	1.00[EUR][1000 genomes]
rs73983727	0.94[ASN][1000 genomes]
rs7564882	1.00[EUR][1000 genomes]
rs7569723	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574324	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576852	1.00[EUR][1000 genomes]
rs7580715	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7581075	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7587752	0.94[ASN][1000 genomes]
rs7605498	1.00[EUR][1000 genomes]
rs893253	1.00[EUR][1000 genomes]
rs893255	1.00[EUR][1000 genomes]
rs893256	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9283521	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288392	0.94[ASN][1000 genomes]
rs934712	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934714	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959660	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs959855	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962595	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap]
rs9646839	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs976247	1.00[EUR][1000 genomes]
rs994696	1.00[EUR][1000 genomes]
rs994697	1.00[EUR][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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv875752	chr2:209141066-209235373	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16840898	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209139400-209180000	Strong transcription	Fetal Thymus	thymus
2	chr2:209141200-209180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:209147400-209225600	Weak transcription	Stomach Mucosa	stomach
4	chr2:209149600-209179800	Strong transcription	Dnd41	blood
5	chr2:209156000-209180000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:209159200-209182200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:209159800-209179400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:209160000-209188800	Weak transcription	Small Intestine	intestine
9	chr2:209162400-209174600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:209163000-209187400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr2:209163200-209177000	Strong transcription	Primary hematopoietic stem cells	blood
12	chr2:209163200-209180600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:209163200-209187400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr2:209163400-209174600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:209163400-209180600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:209163400-209187400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:209163600-209180600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:209163600-209182200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:209164800-209179400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:209165800-209180000	Weak transcription	Aorta	Aorta
21	chr2:209165800-209204000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:209166200-209189600	Weak transcription	Pancreas	Pancrea
23	chr2:209166600-209189000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr2:209167000-209179600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr2:209167200-209176600	Weak transcription	Fetal Heart	heart
26	chr2:209167200-209177400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr2:209167200-209179600	Weak transcription	NHEK	skin
28	chr2:209169800-209180000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:209170000-209176400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:209170000-209178400	Weak transcription	Fetal Stomach	stomach
31	chr2:209170000-209179000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:209170000-209179000	Weak transcription	Lung	lung
33	chr2:209170000-209179000	Weak transcription	Thymus	Thymus
34	chr2:209170000-209179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:209170000-209179200	Weak transcription	A549	lung
36	chr2:209170000-209179400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:209170000-209179400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:209170000-209179400	Weak transcription	Gastric	stomach
39	chr2:209170000-209179600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:209170000-209179600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:209170000-209179800	Weak transcription	Fetal Brain Male	brain
42	chr2:209170000-209179800	Weak transcription	Ovary	ovary
43	chr2:209170000-209179800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr2:209170000-209179800	Weak transcription	Hela-S3	cervix
45	chr2:209170000-209180000	Weak transcription	Esophagus	oesophagus
46	chr2:209170000-209182200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:209170000-209182200	Weak transcription	Spleen	Spleen
48	chr2:209170000-209183000	Weak transcription	Psoas Muscle	Psoas
49	chr2:209170000-209190000	Weak transcription	Right Ventricle	heart
50	chr2:209170200-209175800	Weak transcription	Colon Smooth Muscle	Colon

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