Variant report

Variant	rs1555431
Chromosome Location	chr6:25057429-25057430
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10946746	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12214056	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs303034	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303898	0.89[CHB][hapmap]
rs303899	0.89[CHB][hapmap]
rs303900	0.89[CHB][hapmap]
rs460400	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6916014	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9356960	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9358829	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9358831	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379708	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379711	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9379712	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9379714	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393611	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461094	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1555431	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25046000-25062400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:25049600-25058200	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr6:25049600-25059200	Enhancers	Primary B cells from peripheral blood	blood
4	chr6:25050200-25057800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr6:25050200-25058000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:25050200-25058200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr6:25050600-25059200	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:25051200-25061600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:25054200-25061400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:25054200-25061400	Weak transcription	Lung	lung
11	chr6:25054400-25057800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:25055000-25058000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:25055000-25060400	Weak transcription	Adipose Nuclei	Adipose
14	chr6:25055000-25061400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:25055400-25061200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:25055400-25064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:25055600-25057600	Weak transcription	NHDF-Ad	bronchial
18	chr6:25055800-25057800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:25056000-25057600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:25056000-25057600	Enhancers	Thymus	Thymus
21	chr6:25056000-25057600	Enhancers	Spleen	Spleen
22	chr6:25056000-25057800	Enhancers	Fetal Thymus	thymus
23	chr6:25056000-25058000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:25056000-25058000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:25056600-25057600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:25056600-25061400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:25056600-25061600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:25056800-25057800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr6:25056800-25057800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:25056800-25058000	Enhancers	Primary T cells from cord blood	blood
31	chr6:25056800-25058000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr6:25056800-25058000	Enhancers	Dnd41	blood
33	chr6:25056800-25058200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr6:25056800-25058200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr6:25056800-25059200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:25056800-25059200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr6:25056800-25059200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr6:25056800-25059600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr6:25057000-25058000	Enhancers	Fetal Stomach	stomach
40	chr6:25057000-25059400	Enhancers	Primary B cells from cord blood	blood
41	chr6:25057200-25057600	Enhancers	Fetal Lung	lung
42	chr6:25057200-25057800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:25057200-25058800	Weak transcription	GM12878-XiMat	blood
44	chr6:25057400-25057600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:25057400-25057600	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr6:25057400-25057600	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr6:25057400-25057800	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:25057400-25057800	Enhancers	Fetal Muscle Trunk	muscle
49	chr6:25057400-25057800	Enhancers	Fetal Muscle Leg	muscle
50	chr6:25057400-25057800	Enhancers	Placenta	Placenta

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