Variant report

Variant	rs12525405
Chromosome Location	chr6:25050631-25050632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11757374	0.84[CHD][hapmap];0.85[MEX][hapmap]
rs12524842	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525328	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12528227	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661796	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663160	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195161	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13196712	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203073	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13218879	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447243	0.80[ASN][1000 genomes]
rs1562422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1597011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597012	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160034	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1900551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923192	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923193	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192773	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2273671	0.82[CEU][hapmap];0.84[CHD][hapmap];0.89[MEX][hapmap];1.00[YRI][hapmap]
rs302992	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs303879	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs303880	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs303884	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34322558	0.84[EUR][1000 genomes]
rs34475409	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34693126	0.90[ASN][1000 genomes]
rs35028017	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35553146	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36030790	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792974	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs3792983	0.82[CEU][hapmap];0.87[CHD][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap]
rs3812108	0.84[CHD][hapmap];0.85[MEX][hapmap]
rs4711071	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711072	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711073	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712882	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56108659	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66577954	0.80[ASN][1000 genomes]
rs67240854	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67795839	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738141	0.82[CEU][hapmap];0.87[CHD][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap]
rs895676	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348660	0.80[ASN][1000 genomes]
rs9358827	0.94[JPT][hapmap]
rs9461093	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	esv10579	chr6:25045015-25053354	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12525405	SLC17A4	cis	cerebellum	SCAN
rs12525405	HIST1H1E	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25043200-25053400	Weak transcription	Spleen	Spleen
2	chr6:25043400-25050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:25046000-25062400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:25049600-25050800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:25049600-25058200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr6:25049600-25059200	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:25049800-25050800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:25049800-25051000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr6:25049800-25051200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:25049800-25051800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr6:25049800-25056000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr6:25049800-25056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:25050000-25051200	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr6:25050000-25051800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:25050000-25052000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr6:25050000-25052200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr6:25050000-25052800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr6:25050000-25052800	Enhancers	Dnd41	blood
19	chr6:25050000-25056200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:25050200-25051200	Enhancers	Fetal Brain Male	brain
21	chr6:25050200-25051200	Enhancers	Rectal Smooth Muscle	rectum
22	chr6:25050200-25051600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:25050200-25051800	Enhancers	Primary T cells from cord blood	blood
24	chr6:25050200-25051800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:25050200-25052400	Enhancers	Primary B cells from cord blood	blood
26	chr6:25050200-25052600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr6:25050200-25052800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:25050200-25053000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:25050200-25057800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:25050200-25058000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:25050200-25058200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr6:25050400-25050800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:25050400-25051000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:25050400-25051200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:25050400-25051400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr6:25050400-25051600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr6:25050400-25051600	Enhancers	HUVEC	blood vessel
38	chr6:25050400-25051800	Enhancers	Osteobl	bone
39	chr6:25050400-25052400	Enhancers	GM12878-XiMat	blood
40	chr6:25050400-25054400	Enhancers	Placenta Amnion	Placenta Amnion
41	chr6:25050400-25054600	Enhancers	NHDF-Ad	bronchial
42	chr6:25050400-25056000	Weak transcription	Thymus	Thymus
43	chr6:25050600-25050800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:25050600-25051000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr6:25050600-25051000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:25050600-25051200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:25050600-25055400	Enhancers	Placenta	Placenta
48	chr6:25050600-25059200	Enhancers	Primary hematopoietic stem cells	blood

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