Variant report

Variant	rs3823430
Chromosome Location	chr6:38750888-38750889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38745585..38748255-chr6:38749939..38751759,3	K562	blood:
2	chr6:38745585..38748402-chr6:38749939..38752656,4	K562	blood:
3	chr6:38749592..38751313-chr6:38753149..38755340,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12211240	0.91[ASN][1000 genomes]
rs12665115	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13196567	0.83[EUR][1000 genomes]
rs13209006	0.91[ASN][1000 genomes]
rs13209011	0.91[ASN][1000 genomes]
rs34746318	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35767740	0.83[EUR][1000 genomes]
rs35913247	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4714180	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4714181	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4714182	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4714183	1.00[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6921238	0.80[CEU][hapmap]
rs71571350	0.83[EUR][1000 genomes]
rs7738555	0.90[YRI][hapmap]
rs7739708	0.88[YRI][hapmap]
rs7756191	0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9357283	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs9357284	0.89[CEU][hapmap];0.84[JPT][hapmap]
rs9369082	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9380772	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9380775	0.91[ASN][1000 genomes]
rs9380777	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380778	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9380779	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9380780	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9380782	1.00[CEU][hapmap]
rs9380784	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs9394536	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9394539	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv830643	chr6:38726675-38905589	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv462915	chr6:38728142-38773293	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv602959	chr6:38728142-38786528	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv470814	chr6:38728142-38790149	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv462916	chr6:38747770-38782401	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv602960	chr6:38747770-38782401	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3823430	TBC1D22B	cis	parietal	SCAN
rs3823430	TBCC	cis	cerebellum	SCAN
rs3823430	CTDSPL2	trans	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38750400-38751000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:38750400-38751000	Flanking Active TSS	K562	blood
3	chr6:38750400-38751800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:38750800-38752600	Enhancers	Fetal Kidney	kidney

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