Variant report

Variant	rs9387532
Chromosome Location	chr6:118320108-118320109
allele	A/G
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	SP1	chr6:118320014-118320219	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr6:118320061-118320758	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:118320086-118320624	GM12891	blood:	n/a	n/a
4	GATA2	chr6:118320037-118320409	K562	blood:	n/a	n/a
5	POLR2A	chr6:118319987-118320841	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr6:118320106-118320812	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:118320041-118320798	GM12892	blood:	n/a	n/a
8	SIN3AK20	chr6:118320051-118320185	H1-hESC	embryonic stem cell:	n/a	n/a
9	HEY1	chr6:118320051-118320559	K562	blood:	n/a	n/a
10	POLR2A	chr6:118320086-118320342	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr6:118320023-118320812	GM12892	blood:	n/a	n/a
12	POLR2A	chr6:118320030-118320778	GM12892	blood:	n/a	n/a
13	ZBTB33	chr6:118319907-118320776	K562	blood:	n/a	n/a
14	CTCF	chr6:118320046-118320185	T-47D	breast:	n/a	n/a
15	POLR2A	chr6:118320105-118320782	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000230202	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13198431	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13211121	0.80[AMR][1000 genomes]
rs1338971	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17079625	0.82[ASW][hapmap];0.83[CEU][hapmap];0.92[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2211099	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2355798	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34358304	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36172496	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4113075	0.87[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4120871	0.96[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4245490	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4434501	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4945604	1.00[ASW][hapmap];1.00[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];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4946312	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5002415	0.87[CEU][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs6914871	1.00[ASW][hapmap];0.91[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];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6928714	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6935258	0.83[AMR][1000 genomes]
rs6935516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7744988	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9374693	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9374698	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9385026	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9401043	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9401045	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9481751	0.87[CEU][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]
rs9766457	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9968789	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv981179	chr6:118317043-118324199	Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9387532	SLC35F1	cis	cerebellum	SCAN
rs9387532	PLN	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118315400-118324400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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