Variant report

Variant	rs9566446
Chromosome Location	chr13:40077958-40077959
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1040962	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182780	0.92[CEU][hapmap]
rs4569130	0.92[CEU][hapmap]
rs4941928	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563706	0.92[CEU][hapmap]
rs6563708	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs6563710	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7319652	0.92[CEU][hapmap]
rs7334760	0.96[CEU][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs7337916	0.92[CEU][hapmap]
rs737645	0.92[CEU][hapmap]
rs7996782	0.92[CEU][hapmap]
rs7998182	0.92[CEU][hapmap]
rs943568	0.92[CEU][hapmap]
rs9532382	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9532383	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs9548779	0.96[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs9576810	0.92[CEU][hapmap]

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
rs9566446	RFXAP	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40061600-40081000	Weak transcription	Osteobl	bone
2	chr13:40064800-40081200	Weak transcription	HSMMtube	muscle
3	chr13:40067800-40078400	Enhancers	Fetal Heart	heart
4	chr13:40068400-40080800	Weak transcription	Fetal Brain Female	brain
5	chr13:40069200-40080400	Weak transcription	Aorta	Aorta
6	chr13:40073000-40081200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:40073800-40081200	Weak transcription	Esophagus	oesophagus
8	chr13:40073800-40084200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr13:40074200-40081000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr13:40074200-40094400	Weak transcription	Adipose Nuclei	Adipose
11	chr13:40074600-40080600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr13:40076200-40081000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr13:40076400-40079200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr13:40076400-40079800	Weak transcription	Psoas Muscle	Psoas
15	chr13:40076400-40080400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:40076400-40080400	Weak transcription	Fetal Brain Male	brain
17	chr13:40076400-40080800	Weak transcription	Fetal Lung	lung
18	chr13:40076400-40081000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:40076400-40081000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr13:40076400-40081200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr13:40076400-40081200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:40076400-40081200	Weak transcription	Colon Smooth Muscle	Colon
23	chr13:40076400-40081200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr13:40076400-40081400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr13:40076400-40084000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr13:40076400-40084000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr13:40076400-40089000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr13:40076400-40096000	Weak transcription	Lung	lung
29	chr13:40076600-40079800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr13:40076600-40081200	Weak transcription	Fetal Muscle Leg	muscle
31	chr13:40077200-40081000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr13:40077400-40079600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr13:40077400-40081200	Weak transcription	Ovary	ovary
34	chr13:40077400-40088400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr13:40077400-40088400	Weak transcription	Right Atrium	heart
36	chr13:40077600-40079600	Weak transcription	Placenta	Placenta
37	chr13:40077600-40080400	Weak transcription	Left Ventricle	heart
38	chr13:40077600-40080600	Weak transcription	Right Ventricle	heart
39	chr13:40077600-40088400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr13:40077600-40101400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:40077800-40079200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr13:40077800-40080400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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