Variant report

Variant	rs548342
Chromosome Location	chr6:44401301-44401302
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10807300	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1293205	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1293208	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1296018	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1952979	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2273667	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes]
rs2297331	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2297333	0.81[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2894572	0.89[AMR][1000 genomes]
rs34264814	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34753552	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4143678	0.95[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.99[MKK][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711781	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs475426	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs525043	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs526851	0.96[ASN][1000 genomes]
rs532492	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs545455	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557470	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs559035	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs566078	0.84[JPT][hapmap]
rs67182313	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6918742	0.82[CHD][hapmap]
rs6923521	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6942323	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs864127	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9369488	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9395016	0.88[AMR][1000 genomes]
rs9395017	0.90[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.88[AMR][1000 genomes]
rs9462984	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9462985	0.94[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9462989	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9472273	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[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	nsv1019145	chr6:44313576-44421440	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv885858	chr6:44385441-44421240	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv885859	chr6:44385441-44422466	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv517370	chr6:44385441-44422689	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1850024	chr6:44388505-44422689	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs548342	CD2AP	cis	cerebellum	SCAN
rs548342	RUNX2	cis	cerebellum	SCAN
rs548342	CDC5L	cis	parietal	SCAN
rs548342	GPR115	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44358400-44403800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr6:44376800-44424400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:44385200-44403200	Weak transcription	Gastric	stomach
4	chr6:44386600-44409200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:44386800-44402600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:44386800-44402600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:44386800-44402800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr6:44386800-44404200	Strong transcription	Fetal Thymus	thymus
9	chr6:44386800-44405000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:44386800-44406400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:44386800-44408800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr6:44387000-44401600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:44387000-44401600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:44387000-44402400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr6:44387000-44402600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:44387000-44402600	Strong transcription	Placenta	Placenta
17	chr6:44387000-44402800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:44387000-44403400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:44387000-44403600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:44387000-44405000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr6:44387000-44405400	Strong transcription	Primary hematopoietic stem cells	blood
22	chr6:44387000-44408000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr6:44387200-44402800	Strong transcription	Primary B cells from cord blood	blood
24	chr6:44387400-44403800	Strong transcription	Dnd41	blood
25	chr6:44387600-44408600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:44388400-44424400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:44388800-44403200	Weak transcription	Pancreas	Pancrea
28	chr6:44388800-44409800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:44390000-44404600	Weak transcription	Stomach Mucosa	stomach
30	chr6:44390200-44401800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:44390200-44402200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr6:44390200-44409600	Weak transcription	Spleen	Spleen
33	chr6:44390200-44420200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:44390400-44403400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:44391800-44409800	Weak transcription	Aorta	Aorta
36	chr6:44391800-44412600	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:44392800-44403200	Weak transcription	Psoas Muscle	Psoas
38	chr6:44392800-44407000	Weak transcription	Ovary	ovary
39	chr6:44392800-44411800	Weak transcription	Esophagus	oesophagus
40	chr6:44393400-44401600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:44393600-44401600	Weak transcription	NH-A	brain
42	chr6:44393600-44411600	Weak transcription	Right Ventricle	heart
43	chr6:44394600-44407800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:44394800-44410000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr6:44395200-44407000	Weak transcription	NHEK	skin
46	chr6:44395200-44407200	Weak transcription	HMEC	breast
47	chr6:44395400-44408800	Weak transcription	HUVEC	blood vessel
48	chr6:44396600-44407000	Weak transcription	Osteobl	bone
49	chr6:44396600-44432800	Weak transcription	Fetal Kidney	kidney
50	chr6:44397200-44409800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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