Variant report

Variant	rs9532383
Chromosome Location	chr13:40071315-40071316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1040962	0.92[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs2148933	0.80[EUR][1000 genomes]
rs2182780	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs2182781	0.80[EUR][1000 genomes]
rs4569130	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4941928	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4943666	0.80[EUR][1000 genomes]
rs6563706	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[EUR][1000 genomes]
rs6563707	0.82[EUR][1000 genomes]
rs6563708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563710	0.91[JPT][hapmap];0.91[EUR][1000 genomes]
rs7319652	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs7322023	0.80[EUR][1000 genomes]
rs7326279	1.00[JPT][hapmap]
rs7334760	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7337916	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs737645	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7996782	0.92[CEU][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7998182	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs8000420	1.00[JPT][hapmap]
rs943568	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs9532382	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs9548779	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	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs9576810	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs9603544	1.00[JPT][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
rs9532383	RFXAP	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40059000-40073000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:40060800-40071800	Weak transcription	HSMM	muscle
3	chr13:40061600-40081000	Weak transcription	Osteobl	bone
4	chr13:40062600-40073000	Weak transcription	Psoas Muscle	Psoas
5	chr13:40064800-40081200	Weak transcription	HSMMtube	muscle
6	chr13:40065600-40075000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:40065600-40075200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:40067200-40074000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr13:40067600-40071800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr13:40067600-40072400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr13:40067600-40074000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr13:40067600-40074200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:40067800-40078400	Enhancers	Fetal Heart	heart
14	chr13:40068400-40080800	Weak transcription	Fetal Brain Female	brain
15	chr13:40068600-40072200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr13:40068600-40072400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr13:40068600-40073400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr13:40068600-40073600	Weak transcription	Brain Substantia Nigra	brain
19	chr13:40069200-40075000	Weak transcription	Lung	lung
20	chr13:40069200-40080400	Weak transcription	Aorta	Aorta
21	chr13:40070000-40071400	Enhancers	H9 Cell Line	embryonic stem cell
22	chr13:40070000-40071600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:40070000-40072400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr13:40070000-40072600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr13:40070000-40073000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr13:40070000-40073000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr13:40070200-40071400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr13:40070200-40073000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr13:40070200-40073800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr13:40070400-40071400	Enhancers	Right Ventricle	heart
31	chr13:40070600-40071400	Enhancers	Brain Germinal Matrix	brain
32	chr13:40070800-40071400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr13:40070800-40071400	Enhancers	Right Atrium	heart
34	chr13:40070800-40071600	Enhancers	Ovary	ovary
35	chr13:40071000-40071800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr13:40071000-40072400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:40071000-40073000	Weak transcription	Fetal Muscle Leg	muscle
38	chr13:40071000-40073800	Weak transcription	Adipose Nuclei	Adipose
39	chr13:40071200-40071400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr13:40071200-40071800	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr13:40071200-40072200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr13:40071200-40073000	Weak transcription	Left Ventricle	heart
43	chr13:40071200-40073600	Weak transcription	Fetal Brain Male	brain

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