Variant report

Variant	rs30196
Chromosome Location	chr5:75377551-75377552
allele	A/C
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	POLR2A	chr5:75377388-75378440	H1-neurons	neurons:	n/a	n/a
2	SUZ12	chr5:75377533-75378254	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr5:75377350-75381483	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
SV2C	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs13162056	0.94[EUR][1000 genomes]
rs13174796	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1393205	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1423103	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1423104	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1501905	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap]
rs1553310	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs183766	0.94[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs183767	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs187285	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1910051	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2254153	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2547455	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2547456	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs258612	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs258613	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs258614	0.84[CEU][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs258621	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2731732	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2731733	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2731735	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28620	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28621	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2937705	0.81[CEU][hapmap];0.90[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs30191	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30192	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30197	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30198	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30199	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs30202	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30204	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30205	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30206	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs30249	0.81[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7378518	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7443455	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs993914	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv869885	chr5:75365786-75419656	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1033350	chr5:75367809-75538460	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs30196	CTC-235G5.3	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75376800-75377600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:75377400-75377600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
3	chr5:75377400-75377800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr5:75377400-75381400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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