Variant report

Variant	rs6702809
Chromosome Location	chr1:211114607-211114608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:211109430..211112551-chr1:211113877..211116492,3	K562	blood:
2	chr1:211113979..211116168-chr1:211116520..211118696,2	K562	blood:
3	chr1:211113880..211115899-chr1:211118245..211120568,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10779547	0.92[AFR][1000 genomes]
rs10779548	0.81[CEU][hapmap]
rs10863871	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119636	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119639	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1354112	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs1393029	0.81[CEU][hapmap]
rs1501547	0.92[AFR][1000 genomes]
rs1501553	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1501554	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1501561	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1542887	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs1546277	0.96[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1566602	0.87[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1777242	0.86[CEU][hapmap];0.82[YRI][hapmap]
rs1846946	0.87[ASW][hapmap];0.81[CEU][hapmap]
rs1875437	0.81[CEU][hapmap]
rs2062673	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2088877	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2102129	0.80[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2202095	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2358092	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2358115	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2358117	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4639824	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4951491	0.86[CEU][hapmap]
rs4951700	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4951701	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4951702	0.87[ASW][hapmap];0.81[CEU][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4951704	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4951706	1.00[YRI][hapmap]
rs4951708	0.82[AFR][1000 genomes]
rs6686447	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6692020	0.81[CEU][hapmap]
rs7415388	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7547937	0.92[AFR][1000 genomes]
rs924567	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs924568	0.87[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9662077	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs973945	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs985382	0.81[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873154	chr1:211057697-211117197	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6702809	CD46	cis	cerebellum	SCAN
rs6702809	IKBKE	cis	parietal	SCAN
rs6702809	PLXNA2	cis	parietal	SCAN
rs6702809	SERTAD4	cis	cerebellum	SCAN
rs6702809	C1orf74	cis	parietal	SCAN
rs6702809	NSL1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211108600-211117400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:211112200-211124000	Weak transcription	HSMMtube	muscle
3	chr1:211112400-211120000	Weak transcription	HSMM	muscle
4	chr1:211112800-211124800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:211114600-211115800	Enhancers	Pancreas	Pancrea

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