Variant report

Variant	rs11202902
Chromosome Location	chr10:90693537-90693538
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAS-3	chr10:90692780-90693638	NONHSAT015483

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1008719	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10749596	0.86[MEX][hapmap]
rs10887867	0.84[CEU][hapmap]
rs10887870	0.85[EUR][1000 genomes]
rs11202890	0.84[CEU][hapmap]
rs11202897	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11202898	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11202899	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11202901	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11202906	0.91[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs11202907	0.91[CEU][hapmap];0.85[TSI][hapmap]
rs11591231	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11595119	0.89[CEU][hapmap]
rs11596205	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1214564	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12241401	0.99[EUR][1000 genomes]
rs12248284	0.84[CEU][hapmap]
rs12254084	0.91[CEU][hapmap]
rs12254856	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12267680	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1411780	1.00[CHD][hapmap]
rs17114152	0.84[CEU][hapmap]
rs17114327	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs2119685	0.91[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2439707	0.91[CEU][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2481918	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs303525	1.00[CHD][hapmap]
rs303526	1.00[CHD][hapmap]
rs41284106	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41317244	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4431933	0.84[CEU][hapmap]
rs45493098	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56104559	1.00[EUR][1000 genomes]
rs56228317	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56268252	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57807025	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59737591	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66478243	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7078383	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7085698	0.91[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs7090631	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7098235	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs72809310	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72809311	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72809314	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72809318	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72809335	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72809337	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72809342	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7897521	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7915393	0.91[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs988584	1.00[AMR][1000 genomes];0.96[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	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90655200-90701400	Weak transcription	Gastric	stomach
2	chr10:90660400-90695000	Weak transcription	Fetal Brain Male	brain
3	chr10:90664200-90694600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr10:90664400-90694800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr10:90668400-90694800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr10:90675800-90696400	Weak transcription	Spleen	Spleen
7	chr10:90678000-90694800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr10:90681400-90697800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:90682000-90694800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr10:90683800-90694800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:90684800-90694800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr10:90685800-90695000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:90686000-90694800	Weak transcription	Stomach Mucosa	stomach
14	chr10:90686000-90697600	Weak transcription	Left Ventricle	heart
15	chr10:90686200-90694600	Weak transcription	Fetal Kidney	kidney
16	chr10:90686600-90694800	Weak transcription	Brain Substantia Nigra	brain
17	chr10:90686800-90694800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr10:90686800-90694800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr10:90686800-90694800	Weak transcription	Liver	Liver
20	chr10:90686800-90697800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr10:90687000-90695000	Weak transcription	Primary B cells from cord blood	blood
22	chr10:90687400-90694600	Weak transcription	HSMMtube	muscle
23	chr10:90687400-90694800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr10:90687400-90695000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr10:90687600-90694800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr10:90687600-90694800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr10:90687600-90694800	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr10:90687600-90694800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr10:90687600-90694800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:90687600-90694800	Weak transcription	Fetal Thymus	thymus
31	chr10:90687600-90694800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:90687800-90694800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr10:90688200-90694800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr10:90688200-90694800	Weak transcription	Dnd41	blood
35	chr10:90688600-90694800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr10:90688800-90694800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr10:90689200-90694800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr10:90689200-90695000	Weak transcription	Primary T cells from cord blood	blood
39	chr10:90689400-90694800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr10:90689400-90694800	Weak transcription	HSMM	muscle
41	chr10:90690200-90694600	Weak transcription	Fetal Heart	heart
42	chr10:90691400-90697800	Weak transcription	Small Intestine	intestine
43	chr10:90691800-90694600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr10:90692000-90694800	Weak transcription	Esophagus	oesophagus
45	chr10:90692400-90694800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr10:90692400-90694800	Weak transcription	NH-A	brain
47	chr10:90692400-90695000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:90692400-90695000	Weak transcription	Lung	lung
49	chr10:90692400-90695000	Weak transcription	Ovary	ovary
50	chr10:90692400-90699200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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