Variant report

Variant	rs6453231
Chromosome Location	chr5:75856455-75856456
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10041515	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10043064	0.87[AMR][1000 genomes]
rs10044679	0.82[AMR][1000 genomes]
rs10044688	0.81[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10051729	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10054114	0.80[EUR][1000 genomes]
rs10064543	0.89[JPT][hapmap]
rs10065424	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10073592	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10080190	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10474482	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10942784	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12513951	0.89[JPT][hapmap]
rs13355881	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1501690	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2134190	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2173926	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2202113	0.90[JPT][hapmap]
rs2202114	0.88[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2840106	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3776768	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3797380	0.89[JPT][hapmap]
rs4704326	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4704330	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704332	0.87[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704333	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4704336	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6453232	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6869692	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6889411	0.94[JPT][hapmap]
rs7713954	0.82[AMR][1000 genomes]
rs7722711	0.94[JPT][hapmap]
rs905162	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs905163	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs905164	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9293687	0.89[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9293688	0.84[JPT][hapmap]
rs9654416	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9686939	0.82[AMR][1000 genomes];0.85[EUR][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:46 , 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	chr5:75844800-75857200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:75844800-75857400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr5:75845000-75858200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:75845400-75876600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:75845600-75857200	Weak transcription	Gastric	stomach
9	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:75848600-75857000	Weak transcription	Stomach Mucosa	stomach
11	chr5:75849800-75857200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:75851600-75861200	Weak transcription	Thymus	Thymus
13	chr5:75851800-75857200	Weak transcription	Esophagus	oesophagus
14	chr5:75851800-75858000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:75851800-75860200	Weak transcription	HepG2	liver
16	chr5:75851800-75892000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr5:75852000-75864400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:75852600-75857000	Weak transcription	K562	blood
19	chr5:75852800-75857600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:75852800-75858400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr5:75852800-75860400	Weak transcription	Fetal Intestine Small	intestine
22	chr5:75852800-75877800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr5:75852800-75877800	Weak transcription	Small Intestine	intestine
24	chr5:75853000-75856600	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:75853000-75857200	Weak transcription	Pancreas	Pancrea
26	chr5:75853000-75857400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:75853000-75858400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:75853000-75858400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:75853200-75857600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:75853200-75896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr5:75853400-75857200	Weak transcription	GM12878-XiMat	blood
32	chr5:75853400-75858000	Weak transcription	Primary B cells from cord blood	blood
33	chr5:75853400-75858600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr5:75854600-75863000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr5:75854800-75858800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr5:75855400-75859000	Strong transcription	Primary T cells from cord blood	blood
37	chr5:75855800-75857200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:75855800-75857200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:75855800-75857400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:75855800-75862400	Weak transcription	Fetal Thymus	thymus
41	chr5:75856000-75856800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr5:75856000-75857000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:75856200-75859800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr5:75856200-75860200	Weak transcription	Fetal Stomach	stomach
45	chr5:75856400-75858400	Enhancers	Liver	Liver
46	chr5:75856400-75873000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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