Variant report

Variant	rs4544900
Chromosome Location	chr6:24677988-24677989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11753290	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs17249505	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883593	0.82[CHB][hapmap]
rs1923187	0.87[CEU][hapmap]
rs3181228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344861	0.82[EUR][1000 genomes]
rs6909099	0.92[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs6917209	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6927947	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6928668	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931809	0.92[GIH][hapmap];0.97[TSI][hapmap];0.84[EUR][1000 genomes]
rs6937327	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937533	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757919	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7765904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9356943	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9358791	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358793	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9366577	0.82[CHB][hapmap]
rs9366580	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9379685	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4544900	C6orf62	Cis_1M	lymphoblastoid	RTeQTL
rs4544900	ACOT13	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24668200-24699800	Weak transcription	Brain Substantia Nigra	brain
2	chr6:24668800-24691800	Weak transcription	Psoas Muscle	Psoas
3	chr6:24669000-24681800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:24669000-24686400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:24669000-24690400	Weak transcription	Gastric	stomach
6	chr6:24669000-24693000	Weak transcription	Primary T cells from cord blood	blood
7	chr6:24669000-24701200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr6:24669200-24686200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:24669200-24690800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:24669400-24687600	Weak transcription	Left Ventricle	heart
11	chr6:24669400-24701600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:24671400-24687200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:24674200-24700000	Weak transcription	Fetal Lung	lung
14	chr6:24674600-24683600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:24674600-24703400	Weak transcription	Aorta	Aorta
16	chr6:24674800-24681800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:24674800-24681800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:24674800-24681800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:24674800-24698200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:24674800-24702200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:24674800-24702200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:24674800-24702600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:24675000-24683800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:24675200-24679400	Weak transcription	Fetal Intestine Large	intestine
25	chr6:24675400-24680800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr6:24675600-24683400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr6:24675800-24683600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr6:24676000-24680600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:24676400-24680200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:24676600-24681800	Weak transcription	Thymus	Thymus
31	chr6:24676600-24702600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr6:24677000-24681200	Enhancers	Liver	Liver
33	chr6:24677600-24678200	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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