Variant report

Variant	rs303001
Chromosome Location	chr6:25056769-25056770
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC16A-1	chr6:25056547-25056892	ENSG00000229313.1

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1665820	1.00[ASN][1000 genomes]
rs182499	0.86[ASN][1000 genomes]
rs188567	1.00[CEU][hapmap]
rs302981	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs302985	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303002	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs303003	0.86[ASN][1000 genomes]
rs303005	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303010	1.00[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303011	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs303012	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs416030	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6908916	1.00[GIH][hapmap]
rs7740534	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461103	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs303001	CMAH	Cis_1M	lymphoblastoid	RTeQTL
rs303001	CMAH	cis	multi-tissue	Pritchard

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

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	chr6:25053400-25056800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:25054200-25061400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:25054200-25061400	Weak transcription	Lung	lung
12	chr6:25054400-25057800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:25055000-25058000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:25055000-25060400	Weak transcription	Adipose Nuclei	Adipose
15	chr6:25055000-25061400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr6:25055400-25057200	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:25055400-25057400	Weak transcription	Placenta	Placenta
18	chr6:25055400-25061200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:25055400-25064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:25055600-25057600	Weak transcription	NHDF-Ad	bronchial
21	chr6:25055800-25057800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:25056000-25056800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:25056000-25056800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:25056000-25056800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:25056000-25056800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:25056000-25056800	Flanking Active TSS	Dnd41	blood
27	chr6:25056000-25057000	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr6:25056000-25057200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr6:25056000-25057400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr6:25056000-25057600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr6:25056000-25057600	Enhancers	Thymus	Thymus
32	chr6:25056000-25057600	Enhancers	Spleen	Spleen
33	chr6:25056000-25057800	Enhancers	Fetal Thymus	thymus
34	chr6:25056000-25058000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr6:25056000-25058000	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr6:25056200-25056800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr6:25056200-25056800	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr6:25056200-25056800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr6:25056200-25056800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
40	chr6:25056200-25056800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr6:25056200-25057400	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr6:25056600-25056800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:25056600-25056800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr6:25056600-25056800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:25056600-25056800	Weak transcription	Esophagus	oesophagus
46	chr6:25056600-25057200	Enhancers	GM12878-XiMat	blood
47	chr6:25056600-25057400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr6:25056600-25057600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:25056600-25061400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:25056600-25061600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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