Variant report

Variant	rs2840106
Chromosome Location	chr5:75880324-75880325
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10041515	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10044688	0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10065424	0.83[EUR][1000 genomes]
rs10073592	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10080190	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10474482	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10942784	0.84[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1501690	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2134190	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173926	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2202114	0.80[EUR][1000 genomes]
rs3776768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3822528	0.81[EUR][1000 genomes]
rs4704330	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4704332	0.83[EUR][1000 genomes]
rs4704333	0.82[EUR][1000 genomes]
rs4704336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4704338	0.80[EUR][1000 genomes]
rs6453231	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6453232	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6869692	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6889168	0.82[CEU][hapmap]
rs7735600	0.80[EUR][1000 genomes]
rs905162	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs905163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs905164	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9293687	0.83[EUR][1000 genomes]
rs9654416	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	chr5:75843800-75884400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:75851800-75892000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr5:75853200-75896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr5:75861200-75889600	Weak transcription	Fetal Stomach	stomach
6	chr5:75862200-75885400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr5:75865400-75885800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:75867800-75886000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr5:75868000-75884400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr5:75868000-75885200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:75868000-75885400	Weak transcription	Primary T cells from cord blood	blood
12	chr5:75873600-75903600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:75874000-75892400	Weak transcription	Spleen	Spleen
14	chr5:75874200-75882000	Weak transcription	Esophagus	oesophagus
15	chr5:75875200-75884000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:75877000-75885200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:75877000-75902800	Weak transcription	Adipose Nuclei	Adipose
18	chr5:75877400-75902800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:75879000-75885000	Weak transcription	Placenta	Placenta
20	chr5:75879000-75892400	Weak transcription	Pancreas	Pancrea
21	chr5:75879000-75913600	Weak transcription	Colonic Mucosa	Colon
22	chr5:75879000-75917600	Weak transcription	Fetal Thymus	thymus
23	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
24	chr5:75879200-75881600	Weak transcription	Fetal Lung	lung
25	chr5:75879200-75882400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:75879200-75883400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr5:75879200-75885000	Weak transcription	Primary B cells from cord blood	blood
28	chr5:75879200-75885200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr5:75879200-75885400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr5:75879200-75885400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr5:75879200-75888600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:75879200-75888800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:75879200-75900600	Weak transcription	Fetal Intestine Small	intestine
34	chr5:75879200-75907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr5:75879400-75885400	Weak transcription	Liver	Liver
37	chr5:75879400-75903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr5:75879600-75882800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:75879600-75886800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr5:75879600-75888600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr5:75880000-75880800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr5:75880000-75880800	Enhancers	Stomach Mucosa	stomach
43	chr5:75880000-75881200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:75880200-75880400	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr5:75880200-75880400	Genic enhancers	Gastric	stomach
46	chr5:75880200-75880600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr5:75880200-75880600	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr5:75880200-75880800	Strong transcription	HepG2	liver
49	chr5:75880200-75881800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr5:75880200-75882000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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