Variant report

Variant	rs2909890
Chromosome Location	chr5:75929103-75929104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10035308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10037254	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10042932	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1697844	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1697845	0.87[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2069641	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2431349	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2431350	0.85[ASN][1000 genomes]
rs2431351	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2431353	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2431354	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2431355	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2431357	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2431360	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455219	0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2455221	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2455222	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2455223	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2455224	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2455225	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2455227	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455228	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455230	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455231	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2455232	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs2909889	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2909891	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2937415	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs372390	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797400	0.82[EUR][1000 genomes]
rs3797405	0.82[EUR][1000 genomes]
rs3797409	0.82[EUR][1000 genomes]
rs395661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs410262	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs416451	0.85[ASN][1000 genomes]
rs428121	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs431160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs441157	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs457233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs457717	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs465959	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1031881	chr5:75917033-75946265	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1017025	chr5:75926278-75946265	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
2	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
4	chr5:75903800-75936200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:75903800-75943600	Weak transcription	Spleen	Spleen
6	chr5:75907800-75934600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr5:75913400-75934600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:75914200-75953800	Weak transcription	Colonic Mucosa	Colon
9	chr5:75914400-75932800	Weak transcription	HepG2	liver
10	chr5:75918000-75943400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:75918200-75943600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:75919200-75943600	Weak transcription	Fetal Intestine Large	intestine
13	chr5:75919200-75955400	Weak transcription	Fetal Kidney	kidney
14	chr5:75919400-75938200	Weak transcription	Pancreas	Pancrea
15	chr5:75919400-75944200	Weak transcription	Fetal Lung	lung
16	chr5:75921600-75938000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:75922000-75931000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr5:75922600-75933400	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:75922800-75938000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr5:75923000-75933600	Weak transcription	GM12878-XiMat	blood
21	chr5:75923000-75938000	Weak transcription	Gastric	stomach
22	chr5:75923000-75938400	Weak transcription	Fetal Thymus	thymus
23	chr5:75923000-75944400	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr5:75923200-75933400	Strong transcription	Primary hematopoietic stem cells	blood
25	chr5:75923400-75932400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr5:75923400-75934000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:75923400-75936200	Weak transcription	Fetal Stomach	stomach
28	chr5:75923600-75934400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:75923800-75933200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr5:75924000-75933400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr5:75924200-75929800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:75924200-75930000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr5:75924200-75943600	Weak transcription	Ovary	ovary
34	chr5:75924400-75930400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr5:75924400-75930600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr5:75924600-75930400	Weak transcription	K562	blood
37	chr5:75924800-75936200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr5:75926200-75931400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:75926200-75938000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr5:75926200-75943800	Strong transcription	Primary T cells from cord blood	blood
41	chr5:75926600-75934200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:75927200-75933000	Strong transcription	Primary B cells from cord blood	blood
43	chr5:75927600-75929600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:75927800-75931000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr5:75928000-75929800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:75928000-75931600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:75928200-75929600	Strong transcription	Placenta	Placenta
48	chr5:75928200-75930400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:75928400-75929800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:75928400-75937000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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