Variant report

Variant	rs9548779
Chromosome Location	chr13:40056137-40056138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1040962	0.89[CEU][hapmap];0.88[GIH][hapmap];0.84[EUR][1000 genomes]
rs2011719	0.83[EUR][1000 genomes]
rs2012553	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2148933	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2182780	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2182781	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4340189	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4456371	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4569130	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4941928	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs4943666	0.84[EUR][1000 genomes]
rs6563706	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs6563707	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6563708	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6563710	0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs7319652	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs7322023	0.84[EUR][1000 genomes]
rs7326279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7330999	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7334760	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7337916	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs737645	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7983763	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7985325	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7996782	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7998182	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs8000420	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs943568	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9532382	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs9532383	0.96[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9566446	0.96[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs9576805	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9576807	0.83[EUR][1000 genomes]
rs9576810	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9603544	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	esv2757529	chr13:40040036-40090742	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2759933	chr13:40040036-40090742	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9548779	RFXAP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40041600-40057800	Weak transcription	NHDF-Ad	bronchial
2	chr13:40043600-40068200	Weak transcription	Lung	lung
3	chr13:40046000-40058800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:40046800-40057800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr13:40050000-40057800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr13:40051400-40064400	Weak transcription	HSMMtube	muscle
7	chr13:40051600-40057000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr13:40052000-40057400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr13:40053600-40057800	Weak transcription	NH-A	brain
10	chr13:40054200-40057400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr13:40054200-40057800	Weak transcription	Fetal Heart	heart
12	chr13:40054200-40060600	Weak transcription	Aorta	Aorta
13	chr13:40054400-40057800	Weak transcription	Colon Smooth Muscle	Colon
14	chr13:40054400-40060800	Weak transcription	Fetal Lung	lung
15	chr13:40054800-40057000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr13:40054800-40058200	Weak transcription	Ovary	ovary
17	chr13:40055400-40056200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:40055400-40056400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr13:40055400-40056400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr13:40055600-40056200	Enhancers	H9 Cell Line	embryonic stem cell
21	chr13:40055600-40056200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:40055600-40056200	Enhancers	HUVEC	blood vessel
23	chr13:40055600-40056400	Enhancers	Adipose Nuclei	Adipose
24	chr13:40055600-40056400	Enhancers	Right Ventricle	heart
25	chr13:40055600-40058400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr13:40055600-40060000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:40055800-40058400	Enhancers	Right Atrium	heart
28	chr13:40056000-40056200	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr13:40056000-40056200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr13:40056000-40056400	Weak transcription	Left Ventricle	heart
31	chr13:40056000-40057200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr13:40056000-40057800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:40056000-40058200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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