Variant report

Variant	rs10206684
Chromosome Location	chr2:98467028-98467029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10166513	1.00[ASN][1000 genomes]
rs10167772	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10168543	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10168709	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10169155	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10175129	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176826	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs10180434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180837	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10183768	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10184393	0.87[EUR][1000 genomes]
rs10184457	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10184552	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10188497	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10188713	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10189414	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191101	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10191483	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10192322	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10202138	1.00[ASN][1000 genomes]
rs10208070	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10209970	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10210299	0.83[EUR][1000 genomes]
rs10210520	0.94[ASN][1000 genomes]
rs10210880	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1024086	1.00[CHB][hapmap]
rs11886417	0.94[ASN][1000 genomes]
rs11893437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11894541	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894895	0.94[ASN][1000 genomes]
rs11895170	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs11897301	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712117	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712120	0.94[ASN][1000 genomes]
rs12712147	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12712162	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12712163	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12712172	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992955	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13000585	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004862	0.83[ASN][1000 genomes]
rs13008678	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13008904	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010004	0.94[ASN][1000 genomes]
rs13012645	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13387725	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13404788	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13427422	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1446327	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1503202	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1960329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1982336	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2121271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2293679	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2305142	0.85[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs34190123	1.00[ASN][1000 genomes]
rs34305873	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34414288	0.94[ASN][1000 genomes]
rs34469351	0.90[ASN][1000 genomes]
rs35185431	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35203092	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35402416	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35776557	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35807655	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35940587	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36079497	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821053	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55753459	1.00[ASN][1000 genomes]
rs55817781	0.82[EUR][1000 genomes]
rs6543088	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs6543111	0.91[ASN][1000 genomes]
rs6707719	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6707750	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6712078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6713504	0.84[EUR][1000 genomes]
rs6718982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6721323	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721467	0.81[EUR][1000 genomes]
rs6728312	0.94[ASN][1000 genomes]
rs6736735	0.85[CEU][hapmap]
rs6738401	1.00[ASN][1000 genomes]
rs6751727	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755021	1.00[ASN][1000 genomes]
rs6756969	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6760008	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs68115667	0.94[ASN][1000 genomes]
rs6875	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs71429373	1.00[ASN][1000 genomes]
rs718159	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7557495	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570009	0.94[ASN][1000 genomes]
rs7578638	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7582298	1.00[ASN][1000 genomes]
rs7588227	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7591374	0.87[EUR][1000 genomes]
rs7593290	0.94[ASN][1000 genomes]
rs7594928	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595039	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7599043	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605288	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9784011	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9808558	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9973490	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10206684	INPP4A	cis	cerebellum	SCAN
rs10206684	TEKT4	cis	cerebellum	SCAN
rs10206684	LONRF2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98406400-98469200	Weak transcription	A549	lung
2	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
3	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
4	chr2:98424000-98475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:98428800-98485000	Weak transcription	NHLF	lung
6	chr2:98429000-98470600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:98430000-98467800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:98434200-98484000	Weak transcription	NHDF-Ad	bronchial
9	chr2:98434400-98485800	Weak transcription	Lung	lung
10	chr2:98446000-98475000	Weak transcription	Gastric	stomach
11	chr2:98447800-98479600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:98447800-98502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:98449600-98482000	Weak transcription	Fetal Kidney	kidney
14	chr2:98457000-98477400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:98457000-98477400	Weak transcription	Esophagus	oesophagus
16	chr2:98457000-98478000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:98457000-98485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:98457200-98467600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:98457200-98485800	Weak transcription	Brain Anterior Caudate	brain
20	chr2:98457400-98485800	Weak transcription	Aorta	Aorta
21	chr2:98457600-98468200	Weak transcription	Fetal Thymus	thymus
22	chr2:98457600-98469000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:98457600-98475000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:98457600-98475000	Weak transcription	Fetal Stomach	stomach
25	chr2:98457600-98475000	Weak transcription	Pancreas	Pancrea
26	chr2:98457600-98475000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:98457600-98475000	Weak transcription	Spleen	Spleen
28	chr2:98457600-98475200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:98457600-98477600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:98457600-98485400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:98457800-98467600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:98457800-98467600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:98457800-98467800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:98457800-98473600	Weak transcription	Left Ventricle	heart
35	chr2:98457800-98474800	Weak transcription	Adipose Nuclei	Adipose
36	chr2:98457800-98475000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:98457800-98475200	Weak transcription	Thymus	Thymus
38	chr2:98457800-98478000	Weak transcription	Colonic Mucosa	Colon
39	chr2:98457800-98485200	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:98458000-98468400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:98458000-98475000	Weak transcription	Colon Smooth Muscle	Colon
42	chr2:98458200-98486000	Weak transcription	Ovary	ovary
43	chr2:98458200-98486800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr2:98458400-98468200	Weak transcription	HepG2	liver
45	chr2:98458400-98475000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:98458400-98475000	Weak transcription	Fetal Intestine Large	intestine
47	chr2:98458400-98478000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:98458600-98475000	Weak transcription	Dnd41	blood
49	chr2:98458600-98485600	Weak transcription	Placenta	Placenta
50	chr2:98459200-98477200	Weak transcription	Fetal Lung	lung

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