Variant report

Variant	rs9326152
Chromosome Location	chr1:47488569-47488570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr1:47488552-47489130	U2OS	brain:	n/a	n/a
2	REST	chr1:47488528-47490139	H1-neurons	neurons:	n/a	chr1:47489332-47489345

Variant related genes	Relation type
CYP4X1	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1021827	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1021828	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1039469	0.81[EUR][1000 genomes]
rs10890443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890444	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890445	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890446	0.82[GIH][hapmap]
rs10890457	0.91[MKK][hapmap]
rs10890460	0.91[MKK][hapmap]
rs10890464	0.88[MKK][hapmap]
rs1117514	0.83[AFR][1000 genomes]
rs11211422	0.85[GIH][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];0.89[YRI][hapmap]
rs11211423	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs11211439	0.82[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.82[YRI][hapmap]
rs11211451	0.91[MKK][hapmap]
rs12022635	0.82[GIH][hapmap];0.85[YRI][hapmap]
rs12037014	0.91[MKK][hapmap]
rs12041262	0.89[GIH][hapmap]
rs12141009	0.89[GIH][hapmap]
rs12564635	0.82[GIH][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.85[YRI][hapmap]
rs12734327	0.91[MKK][hapmap]
rs12736235	0.82[GIH][hapmap];0.86[LWK][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1393659	0.83[AFR][1000 genomes]
rs1393667	0.82[GIH][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.91[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1502908	0.83[CEU][hapmap];0.91[MEX][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1502909	0.91[CEU][hapmap];0.89[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1553390	0.89[GIH][hapmap]
rs1553391	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1827473	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs1827474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847222	0.82[YRI][hapmap]
rs1847225	0.83[GIH][hapmap]
rs1963620	0.80[EUR][1000 genomes]
rs1967757	0.91[MKK][hapmap]
rs2036462	0.91[CEU][hapmap];0.91[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2055500	0.89[YRI][hapmap]
rs4448558	0.85[YRI][hapmap]
rs4926785	0.91[MKK][hapmap]
rs4926793	0.91[MKK][hapmap]
rs6664392	0.88[MKK][hapmap]
rs6690005	0.91[MKK][hapmap]
rs7545399	0.88[MKK][hapmap]
rs9326151	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9326153	0.83[AFR][1000 genomes]
rs9699932	0.83[AFR][1000 genomes]
rs9701154	0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9701899	0.83[AFR][1000 genomes]
rs9729662	0.83[AFR][1000 genomes]
rs9793202	0.82[GIH][hapmap];0.82[MEX][hapmap];0.89[YRI][hapmap]
rs9793711	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9793716	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871958	chr1:47350374-47517123	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1009338	chr1:47358532-47555253	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870695	chr1:47363893-47502714	Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv871288	chr1:47363893-47507808	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv871377	chr1:47363893-47517123	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv546166	chr1:47407739-47495605	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv870674	chr1:47416441-47517123	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
10	nsv871717	chr1:47449486-47524264	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv461428	chr1:47487585-47524264	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv546167	chr1:47487585-47524264	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9326152	MOBKL2C	cis	cerebellum	SCAN
rs9326152	C1orf50	cis	parietal	SCAN
rs9326152	GPBP1L1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47484400-47489000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:47487400-47488600	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr1:47487600-47488800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:47487600-47489000	Weak transcription	Aorta	Aorta
5	chr1:47487800-47488600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:47487800-47488800	Weak transcription	Adipose Nuclei	Adipose
7	chr1:47487800-47489000	Weak transcription	Liver	Liver
8	chr1:47487800-47489200	Weak transcription	Lung	lung
9	chr1:47487800-47489200	Weak transcription	Right Atrium	heart
10	chr1:47488400-47488600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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