Variant report

Variant	rs9654416
Chromosome Location	chr5:75886631-75886632
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10041515	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10044688	0.82[AMR][1000 genomes]
rs10051729	0.85[AMR][1000 genomes]
rs10065424	0.81[AMR][1000 genomes]
rs10073592	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10080190	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10474482	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10942784	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1501690	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2134190	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2173926	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2840106	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776768	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4704330	0.81[AMR][1000 genomes]
rs4704332	0.81[AMR][1000 genomes]
rs4704336	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6453231	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6453232	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6869692	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs905162	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs905163	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs905164	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	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
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv598681	chr5:75863987-75902533	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:75851800-75892000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:75853200-75896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:75861200-75889600	Weak transcription	Fetal Stomach	stomach
5	chr5:75873600-75903600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:75874000-75892400	Weak transcription	Spleen	Spleen
7	chr5:75877000-75902800	Weak transcription	Adipose Nuclei	Adipose
8	chr5:75877400-75902800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:75879000-75892400	Weak transcription	Pancreas	Pancrea
10	chr5:75879000-75913600	Weak transcription	Colonic Mucosa	Colon
11	chr5:75879000-75917600	Weak transcription	Fetal Thymus	thymus
12	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
13	chr5:75879200-75888600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr5:75879200-75888800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:75879200-75900600	Weak transcription	Fetal Intestine Small	intestine
16	chr5:75879200-75907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:75879400-75903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr5:75879600-75886800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:75879600-75888600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr5:75880600-75892600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:75880800-75887400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:75880800-75897600	Weak transcription	HepG2	liver
25	chr5:75882000-75901400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
27	chr5:75882800-75892600	Weak transcription	Gastric	stomach
28	chr5:75883400-75904200	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:75884000-75890000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:75884000-75903000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:75884000-75914600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr5:75884200-75902200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:75884400-75890000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:75884400-75919200	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr5:75884400-75919400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:75884800-75887600	Weak transcription	Fetal Brain Male	brain
37	chr5:75885000-75890400	Strong transcription	Placenta	Placenta
38	chr5:75885000-75891200	Strong transcription	Primary B cells from cord blood	blood
39	chr5:75885000-75891200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:75885200-75890200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:75885200-75900800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr5:75885400-75889800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr5:75885400-75890000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr5:75885400-75890200	Strong transcription	Primary T cells from cord blood	blood
45	chr5:75885400-75890400	Strong transcription	Liver	Liver
46	chr5:75885400-75893600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:75885400-75905000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr5:75885600-75887200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr5:75885800-75887200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:75886000-75887000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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