Variant report

Variant	rs17630545
Chromosome Location	chr8:113265869-113265870
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10505178	0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10505180	0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10505181	0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10505182	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10505183	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955620	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12155552	0.81[CHB][hapmap]
rs12155895	0.89[CHB][hapmap]
rs12675142	0.83[CHB][hapmap]
rs12675203	0.84[ASN][1000 genomes]
rs12675392	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12676450	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12677056	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs12677528	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12677631	0.85[CHB][hapmap]
rs12678444	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12680127	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12680536	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12681572	0.85[CHB][hapmap]
rs1388964	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17554221	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17555344	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17556896	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17637578	0.92[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17637608	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17638567	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17640016	0.85[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs17640721	0.85[CHB][hapmap];0.88[CHD][hapmap]
rs2045034	0.85[CHB][hapmap]
rs4540432	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4876463	0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4876466	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs5020695	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55868089	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55964861	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56148035	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56180460	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56298658	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56333610	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56367843	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59341078	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59994716	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs60128946	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs60533422	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61078986	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61189440	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62514381	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62514390	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62514391	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62514398	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62514406	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62514407	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62514408	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62514409	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62514420	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62514422	0.84[ASN][1000 genomes]
rs62514423	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6992196	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs6993441	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7011864	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72672840	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72672881	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72674712	0.84[ASN][1000 genomes]
rs72674718	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72674724	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9297473	0.85[CHB][hapmap];0.88[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533857	chr8:112819659-113801258	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv891322	chr8:112978128-113267916	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1022457	chr8:113071774-113811177	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17630545	CSMD3	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:113259400-113266800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:113264400-113269200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr8:113264600-113268600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr8:113265200-113266200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr8:113265200-113266600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:113265200-113268800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr8:113265200-113269000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr8:113265400-113266200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr8:113265400-113266200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr8:113265400-113266200	Enhancers	NHEK	skin
11	chr8:113265400-113268800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr8:113265600-113266000	Enhancers	HMEC	breast
13	chr8:113265600-113266200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr8:113265600-113266200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr8:113265800-113266200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:113265800-113266800	Weak transcription	H1 Cell Line	embryonic stem cell

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