Variant report

Variant	rs17680732
Chromosome Location	chr5:75857860-75857861
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10462543	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12513400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12513594	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12513678	0.87[ASN][1000 genomes]
rs12519094	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12519329	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12519473	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12521026	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12523647	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1501788	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs1566	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17680756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17680811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17748322	0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2270908	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3736394	0.82[JPT][hapmap]
rs3756514	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3797382	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3797388	1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs3912001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4289539	0.82[ASN][1000 genomes]
rs4703713	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4704329	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4704340	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55699952	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56110610	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56338424	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58087114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60881227	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61014011	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61233297	0.96[ASN][1000 genomes]
rs869733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs873787	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs879017	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:75843800-75884400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:75844400-75860400	Weak transcription	Placenta	Placenta
4	chr5:75845000-75858200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr5:75845400-75876600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:75851600-75861200	Weak transcription	Thymus	Thymus
8	chr5:75851800-75858000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr5:75851800-75860200	Weak transcription	HepG2	liver
10	chr5:75851800-75892000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:75852000-75864400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:75852800-75858400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:75852800-75860400	Weak transcription	Fetal Intestine Small	intestine
14	chr5:75852800-75877800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr5:75852800-75877800	Weak transcription	Small Intestine	intestine
16	chr5:75853000-75858400	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr5:75853000-75858400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:75853200-75896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr5:75853400-75858000	Weak transcription	Primary B cells from cord blood	blood
20	chr5:75853400-75858600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:75854600-75863000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:75854800-75858800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:75855400-75859000	Strong transcription	Primary T cells from cord blood	blood
24	chr5:75855800-75862400	Weak transcription	Fetal Thymus	thymus
25	chr5:75856200-75859800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr5:75856200-75860200	Weak transcription	Fetal Stomach	stomach
27	chr5:75856400-75858400	Enhancers	Liver	Liver
28	chr5:75856400-75873000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr5:75856600-75861600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:75856800-75858800	Enhancers	Fetal Lung	lung
31	chr5:75856800-75860200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr5:75857000-75858600	Enhancers	Stomach Mucosa	stomach
33	chr5:75857000-75863200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:75857200-75858000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr5:75857200-75858200	Enhancers	Pancreas	Pancrea
36	chr5:75857200-75858600	Enhancers	Ovary	ovary
37	chr5:75857200-75858800	Enhancers	GM12878-XiMat	blood
38	chr5:75857200-75859000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr5:75857200-75859200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:75857200-75863200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr5:75857400-75858800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:75857400-75862000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr5:75857400-75866200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:75857600-75861400	Weak transcription	K562	blood
45	chr5:75857600-75863200	Weak transcription	Gastric	stomach
46	chr5:75857600-75863800	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr5:75857600-75864000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:75857800-75858200	Enhancers	Esophagus	oesophagus
49	chr5:75857800-75863800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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