Variant report

Variant	rs550176
Chromosome Location	chr6:25053369-25053370
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs177356	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs303878	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs304256	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304257	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304258	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304259	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs466944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513585	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs516361	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608874	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609408	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs550176	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25043200-25053400	Weak transcription	Spleen	Spleen
2	chr6:25046000-25062400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:25049600-25058200	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr6:25049600-25059200	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:25049800-25056000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:25049800-25056000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr6:25050000-25056200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr6:25050200-25057800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr6:25050200-25058000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:25050200-25058200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr6:25050400-25054400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr6:25050400-25054600	Enhancers	NHDF-Ad	bronchial
13	chr6:25050400-25056000	Weak transcription	Thymus	Thymus
14	chr6:25050600-25055400	Enhancers	Placenta	Placenta
15	chr6:25050600-25059200	Enhancers	Primary hematopoietic stem cells	blood
16	chr6:25050800-25054200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:25051000-25053400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:25051000-25054000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:25051000-25054200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:25051000-25054400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:25051200-25053600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:25051200-25054000	Weak transcription	HSMM	muscle
23	chr6:25051200-25055000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:25051200-25056000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:25051200-25056200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:25051200-25061600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:25051400-25054200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:25051400-25056000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr6:25051400-25056200	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr6:25051600-25053600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:25051600-25053800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr6:25051600-25054200	Weak transcription	HUVEC	blood vessel
33	chr6:25051600-25056000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr6:25051600-25056000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:25051800-25053600	Weak transcription	Osteobl	bone
36	chr6:25051800-25053800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:25051800-25054000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:25051800-25054000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr6:25051800-25054200	Weak transcription	Primary T cells from cord blood	blood
40	chr6:25052000-25054600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:25052200-25053600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr6:25052200-25053600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr6:25052200-25055400	Enhancers	NHLF	lung
44	chr6:25052400-25053400	Weak transcription	Primary B cells from cord blood	blood
45	chr6:25052400-25053400	Weak transcription	GM12878-XiMat	blood
46	chr6:25052400-25053600	Weak transcription	Esophagus	oesophagus
47	chr6:25052600-25053800	Weak transcription	Stomach Mucosa	stomach
48	chr6:25052600-25054800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:25052600-25056000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:25052600-25056200	Weak transcription	Rectal Mucosa Donor 29	rectum

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