Variant report

Variant	rs2239826
Chromosome Location	chr6:167504880-167504881
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 125 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10455982	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10484530	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10484531	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1060404	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs10946203	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10946204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10946207	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10946208	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10946216	0.85[CEU][hapmap]
rs12178491	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12193698	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12203510	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12208359	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12209395	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12212247	0.81[AMR][1000 genomes]
rs12213683	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12523712	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12527827	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12528323	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12528689	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12529238	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12529876	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12529959	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13195812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13204839	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13208636	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13210649	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13213249	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1358882	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1358883	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1407315	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1571878	0.81[CEU][hapmap]
rs17524252	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17615336	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1810644	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2001114	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2001115	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2017338	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2038580	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2181058	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2237272	0.81[AMR][1000 genomes]
rs2237274	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2237276	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2239823	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2239827	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285147	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2285148	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs239935	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3093024	0.84[CEU][hapmap]
rs3093025	0.81[CEU][hapmap]
rs3752520	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs427824	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4710171	0.81[AMR][1000 genomes]
rs4710175	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4710176	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4710185	0.81[CHB][hapmap]
rs62436765	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6456149	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6456150	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6456151	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6456152	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6456153	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6456154	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6900701	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6902119	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6904946	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6905911	1.00[YRI][hapmap]
rs6907666	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs6909180	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6909475	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6909502	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6918286	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6920858	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6921588	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6923582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6932740	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6934043	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6936261	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6941355	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs720325	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7742305	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7748224	0.82[EUR][1000 genomes]
rs7760495	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7761977	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7762156	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7766242	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs911632	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs916331	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9295385	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9457249	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9457251	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9457252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9457256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9457259	0.81[ASN][1000 genomes]
rs9457260	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9457261	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9457268	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9457270	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9457273	1.00[YRI][hapmap]
rs9459836	0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs9459838	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9459840	0.81[ASN][1000 genomes]
rs9459841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9459849	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9459853	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9459854	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9459855	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9459862	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9459871	0.82[AMR][1000 genomes]
rs9459872	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9459874	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
6	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
8	esv2752099	chr6:167448181-167579102	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1018193	chr6:167491589-167797294	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv538544	chr6:167491589-167797294	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv469673	chr6:167500376-167658532	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv482439	chr6:167500376-167658532	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	esv2758094	chr6:167501204-167845935	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	esv2759492	chr6:167501204-168176733	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2239826	RNASET2	cis	Whole Blood	GTEx
rs2239826	AL133458.1	cis	Whole Blood	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167502000-167506000	Enhancers	Primary B cells from peripheral blood	blood
2	chr6:167502800-167506200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr6:167502800-167507400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr6:167503000-167506200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:167503200-167505600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr6:167503200-167508000	Weak transcription	Gastric	stomach
7	chr6:167503200-167509800	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:167503400-167506200	Enhancers	Thymus	Thymus
9	chr6:167503600-167505200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:167503600-167506400	Enhancers	Primary T cells fromperipheralblood	blood
11	chr6:167503600-167506400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr6:167503600-167507200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:167503600-167507600	Weak transcription	Right Atrium	heart
14	chr6:167503600-167527200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:167503800-167506000	Enhancers	Fetal Thymus	thymus
16	chr6:167503800-167506400	Enhancers	Primary T cells from cord blood	blood
17	chr6:167503800-167506600	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr6:167503800-167507400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:167504000-167505200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:167504000-167506200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr6:167504200-167505000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:167504200-167505200	Weak transcription	Placenta	Placenta
23	chr6:167504200-167506600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr6:167504200-167506800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr6:167504200-167507000	Weak transcription	Adipose Nuclei	Adipose
26	chr6:167504200-167507200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr6:167504200-167507400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr6:167504400-167505000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr6:167504400-167505200	Weak transcription	Fetal Muscle Leg	muscle
30	chr6:167504400-167505400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:167504400-167507400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr6:167504600-167505200	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr6:167504600-167505200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr6:167504600-167505600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:167504600-167505800	Enhancers	Spleen	Spleen
36	chr6:167504600-167508000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr6:167504800-167505200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr6:167504800-167505200	Enhancers	GM12878-XiMat	blood

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