Variant report

Variant	rs2327699
Chromosome Location	chr9:3014702-3014703
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	REST	chr9:3013896-3014856	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
CARM1P1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10114357	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123800	0.94[ASN][1000 genomes]
rs10124669	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757938	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757940	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10757941	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10813222	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10813225	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12351816	0.96[ASN][1000 genomes]
rs2327698	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2327701	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3847238	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847239	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847240	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3847241	0.96[ASN][1000 genomes]
rs3847243	0.84[EUR][1000 genomes]
rs3858039	0.86[EUR][1000 genomes]
rs4543592	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4741801	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4741802	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6476180	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6476181	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7031686	0.94[ASN][1000 genomes]
rs7032385	0.94[ASN][1000 genomes]
rs7032665	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7041058	0.86[EUR][1000 genomes]
rs7850845	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854297	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1024262	chr9:2703159-3067931	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv892085	chr9:2937654-3215842	Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1016036	chr9:3003995-3054185	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv831494	chr9:3007268-3172056	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv525902	chr9:3014254-3022906	Enhancers Weak transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
9	nsv892087	chr9:3014702-3153178	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2327699	PDCD1LG2	cis	cerebellum	SCAN
rs2327699	DMRT2	cis	parietal	SCAN
rs2327699	INSL6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3007200-3018200	Weak transcription	Fetal Brain Male	brain
2	chr9:3011600-3015000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr9:3013200-3018400	Weak transcription	Adipose Nuclei	Adipose
4	chr9:3013800-3015200	Enhancers	Stomach Mucosa	stomach
5	chr9:3014200-3018200	Weak transcription	Stomach Smooth Muscle	stomach

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