Variant report

Variant	rs11886417
Chromosome Location	chr2:98575531-98575532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10166513	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10167772	0.94[ASN][1000 genomes]
rs10168543	0.88[ASN][1000 genomes]
rs10175129	0.94[ASN][1000 genomes]
rs10176826	0.85[CHB][hapmap];0.80[YRI][hapmap]
rs10180434	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10180722	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10183768	0.94[ASN][1000 genomes]
rs10184457	0.85[CHB][hapmap]
rs10188497	0.88[ASN][1000 genomes]
rs10188713	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10189414	0.94[ASN][1000 genomes]
rs10191101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191483	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10192322	0.82[CHB][hapmap]
rs10202138	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206684	0.94[ASN][1000 genomes]
rs10209970	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210520	0.88[ASN][1000 genomes]
rs10210880	1.00[ASN][1000 genomes]
rs1024086	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11893437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11894541	0.94[ASN][1000 genomes]
rs11894895	0.88[ASN][1000 genomes]
rs11895170	0.85[CHB][hapmap];0.80[YRI][hapmap]
rs11897301	0.88[ASN][1000 genomes]
rs12712117	0.88[ASN][1000 genomes]
rs12712120	0.88[ASN][1000 genomes]
rs12712162	0.88[ASN][1000 genomes]
rs12712163	0.81[ASN][1000 genomes]
rs12712172	0.94[ASN][1000 genomes]
rs12992955	0.94[ASN][1000 genomes]
rs13000585	0.94[ASN][1000 genomes]
rs13008904	0.94[ASN][1000 genomes]
rs13009300	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13010004	0.88[ASN][1000 genomes]
rs1446327	0.88[ASN][1000 genomes]
rs1960329	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1982336	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2121271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2293679	0.85[CHB][hapmap];0.80[YRI][hapmap]
rs34190123	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs34414288	0.88[ASN][1000 genomes]
rs34469351	0.97[ASN][1000 genomes]
rs35185431	0.88[ASN][1000 genomes]
rs35203092	0.88[ASN][1000 genomes]
rs35589428	0.88[AMR][1000 genomes]
rs35776557	0.90[ASN][1000 genomes]
rs35807655	0.94[ASN][1000 genomes]
rs35940587	1.00[ASN][1000 genomes]
rs36079497	1.00[ASN][1000 genomes]
rs3821053	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs55753459	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6543111	0.85[ASN][1000 genomes]
rs6707719	0.85[CHB][hapmap]
rs6712078	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6718982	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]
rs6721323	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6728312	0.88[ASN][1000 genomes]
rs6738401	0.94[ASN][1000 genomes]
rs6751727	0.94[ASN][1000 genomes]
rs6755021	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6756969	1.00[ASN][1000 genomes]
rs6760008	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.88[ASN][1000 genomes]
rs68115667	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71429373	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs718159	0.88[ASN][1000 genomes]
rs7557495	0.94[ASN][1000 genomes]
rs7570009	0.88[ASN][1000 genomes]
rs7578638	1.00[ASN][1000 genomes]
rs7582298	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7588227	1.00[ASN][1000 genomes]
rs7593290	0.88[ASN][1000 genomes]
rs7594928	0.94[ASN][1000 genomes]
rs7595039	0.88[ASN][1000 genomes]
rs7599043	0.94[ASN][1000 genomes]
rs7605288	1.00[ASN][1000 genomes]
rs9808558	0.85[CHB][hapmap]
rs9973490	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98563600-98589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:98564600-98580600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:98567600-98586600	Weak transcription	Fetal Stomach	stomach
4	chr2:98568000-98578200	Weak transcription	Brain Anterior Caudate	brain
5	chr2:98568000-98583000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:98568200-98580800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:98568400-98586600	Weak transcription	Aorta	Aorta
9	chr2:98568400-98592000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:98569200-98579400	Weak transcription	Esophagus	oesophagus
11	chr2:98569200-98579600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:98569200-98580600	Weak transcription	NHDF-Ad	bronchial
13	chr2:98569200-98581400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:98571000-98579400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:98571000-98586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:98573800-98575600	Enhancers	Fetal Thymus	thymus
17	chr2:98573800-98575800	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:98574000-98575600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:98574000-98575800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:98574000-98575800	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:98574000-98578400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr2:98574200-98575800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr2:98574200-98576000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr2:98574200-98577800	Weak transcription	Brain Substantia Nigra	brain
25	chr2:98574200-98580400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:98574400-98575600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:98574400-98575600	Enhancers	Lung	lung
28	chr2:98574400-98575800	Enhancers	Ovary	ovary
29	chr2:98574400-98575800	Enhancers	Pancreas	Pancrea
30	chr2:98574400-98575800	Enhancers	Right Atrium	heart
31	chr2:98574400-98576000	Enhancers	Psoas Muscle	Psoas
32	chr2:98574400-98586200	Weak transcription	NH-A	brain
33	chr2:98574600-98582200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr2:98574600-98583200	Weak transcription	Primary B cells from cord blood	blood
35	chr2:98574600-98583400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr2:98574800-98575800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr2:98574800-98579200	Weak transcription	Fetal Heart	heart
38	chr2:98574800-98585200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr2:98574800-98586200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:98575000-98578000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:98575000-98583000	Weak transcription	Gastric	stomach
42	chr2:98575000-98585000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:98575000-98586800	Weak transcription	Brain Angular Gyrus	brain
44	chr2:98575000-98589000	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:98575200-98576800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:98575200-98576800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr2:98575200-98576800	Weak transcription	HMEC	breast
48	chr2:98575200-98578200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr2:98575200-98579000	Weak transcription	NHEK	skin
50	chr2:98575200-98579200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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