Variant report

Variant	rs1866046
Chromosome Location	chr2:209194979-209194980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10174541	0.86[AMR][1000 genomes]
rs10177810	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10186350	0.90[CEU][hapmap];0.85[AMR][1000 genomes]
rs10190458	0.80[AMR][1000 genomes]
rs10194539	0.86[AMR][1000 genomes]
rs10198535	0.83[AMR][1000 genomes]
rs10497897	0.88[AMR][1000 genomes]
rs10497898	0.88[AMR][1000 genomes]
rs11538998	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885913	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891163	1.00[ASN][1000 genomes]
rs11895188	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11898653	0.86[AMR][1000 genomes]
rs11901959	0.88[AMR][1000 genomes]
rs11902124	1.00[CHD][hapmap];0.90[GIH][hapmap]
rs12185709	0.89[CEU][hapmap]
rs12475932	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs1259699	1.00[CHD][hapmap]
rs12694104	0.89[CEU][hapmap]
rs12991283	1.00[ASN][1000 genomes]
rs12998277	1.00[ASN][1000 genomes]
rs13395035	1.00[ASN][1000 genomes]
rs13400356	1.00[ASN][1000 genomes]
rs13407268	0.80[AMR][1000 genomes]
rs13412043	0.86[AMR][1000 genomes]
rs1347664	1.00[CHD][hapmap];0.90[GIH][hapmap]
rs1437413	1.00[CHD][hapmap];0.89[GIH][hapmap]
rs16841224	0.90[GIH][hapmap]
rs16841236	1.00[CHD][hapmap]
rs17699838	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700235	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1816612	1.00[CHD][hapmap];0.90[GIH][hapmap]
rs28418905	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28885800	1.00[ASN][1000 genomes]
rs35217101	1.00[ASN][1000 genomes]
rs35293936	1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs4673394	0.90[CEU][hapmap]
rs4675748	0.81[CEU][hapmap]
rs4675751	0.90[CEU][hapmap]
rs59522113	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6435435	1.00[CHD][hapmap]
rs66826643	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66887797	0.85[AMR][1000 genomes]
rs6716615	1.00[CHD][hapmap]
rs6717082	1.00[CHD][hapmap]
rs67171462	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6725418	0.81[CEU][hapmap];0.82[GIH][hapmap];0.82[EUR][1000 genomes]
rs6725527	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67581965	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs67660353	1.00[ASN][1000 genomes]
rs67669827	0.88[AMR][1000 genomes]
rs67965883	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72989243	0.82[AMR][1000 genomes]
rs73056463	0.86[AMR][1000 genomes]
rs73070962	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7557303	0.88[AMR][1000 genomes]
rs999890	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs999891	0.90[CEU][hapmap];1.00[CHD][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes];1.00[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	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
2	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
3	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
rs1866046	INO80D	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209147400-209225600	Weak transcription	Stomach Mucosa	stomach
2	chr2:209165800-209204000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:209179000-209220600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr2:209180600-209224600	Strong transcription	Fetal Thymus	thymus
5	chr2:209182400-209224200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:209184600-209201400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:209185600-209224000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:209188000-209201000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:209188400-209213400	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:209188400-209221400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:209188400-209223400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr2:209188600-209214200	Strong transcription	Placenta	Placenta
13	chr2:209188800-209195800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr2:209188800-209195800	Strong transcription	NHDF-Ad	bronchial
15	chr2:209188800-209196000	Strong transcription	HepG2	liver
16	chr2:209188800-209196200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:209188800-209196200	Strong transcription	Fetal Intestine Large	intestine
18	chr2:209188800-209196400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:209188800-209196400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr2:209188800-209196600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:209188800-209197200	Strong transcription	Osteobl	bone
22	chr2:209188800-209197400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:209188800-209197600	Strong transcription	HSMM	muscle
24	chr2:209188800-209198800	Strong transcription	Liver	Liver
25	chr2:209188800-209208400	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:209188800-209208600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:209188800-209211200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:209188800-209211200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr2:209188800-209212000	Strong transcription	Adipose Nuclei	Adipose
30	chr2:209188800-209212400	Strong transcription	NH-A	brain
31	chr2:209188800-209213200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:209188800-209214000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:209188800-209215400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:209188800-209220400	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr2:209188800-209221200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:209188800-209221200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:209188800-209221800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:209188800-209222200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:209188800-209222400	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:209188800-209222600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:209188800-209223600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:209188800-209223800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr2:209188800-209224000	Strong transcription	Primary B cells from cord blood	blood
44	chr2:209188800-209224000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr2:209188800-209224200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:209188800-209224400	Strong transcription	Dnd41	blood
47	chr2:209189000-209200600	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:209189200-209195200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:209189200-209196000	Strong transcription	A549	lung
50	chr2:209189200-209209000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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